Gulf of Chiriqui benthic cover
Ana M. Palacio-Castro
2021-08-31
- Setup
- 1. Uva reef
- Explore data
- Data analysis (Aggregated data)
- 2. Stacked categories - Supplement? Uva Island
- 3. Supplemantary datasets (Canal del Afuera and Secas)
- Packages used
Setup
1. Uva reef
Import Coral cover data
(Wide format)
# Read data
cover <- read.csv("Data/Uva_cover.csv", header=TRUE, sep = ",")
#summary(cover)
# Convert variables and factors to right format
# convert to numeric variables
cover$Pocillopora <- as.numeric(cover$Pocillopora)
cover$Massive <- as.numeric(cover$Other_scleractinians)
cover$Millepora <- as.numeric(cover$Millepora)
cover$Algae<- as.numeric(cover$Algae)
cover$Substrate<- as.numeric(cover$Substrate)
cover$YEAR <- as.numeric(cover$YEAR)
# convert to nominal factors
cover$Location <- as.factor(cover$Location)
# Dates
# Note: all day from a month were converted to the 15th
cover$Date<-as.Date(cover$Date, format = "%Y-%m-%d")
#summary(cover)Check transects/sample units
Explore data
Pocillopora
- Pre-1982 Pocillopora cover in 4*5 = 77% manually added
- Line = mean
- Boxplots = median
Non-Pocillopora scleractinians (Uva)
- Line = mean
- Boxplots = median
Millepora (Uva)
- Millepora sp. (individual transects)
Data analysis (Aggregated data)
Aggregate data (Pocillopora)
- Hierarchically aggregate by date and location
# Aggregate by Dataset - Month -Year
aggr.location <- aggregate(Pocillopora
~YEAR+Month+Location,
FUN=mean, data=cover)
aggr.location$Year_F<-as.factor(aggr.location$YEAR)
aggr.location$Date<-paste(aggr.location$YEAR, aggr.location$Month, "15", sep = "-")
aggr.location$Date<-as.Date(aggr.location$Date, format = "%Y-%b-%d")
str(aggr.location)## 'data.frame': 89 obs. of 6 variables:
## $ YEAR : num 2016 2017 1984 1985 2014 ...
## $ Month : Factor w/ 12 levels "Apr","Aug","Dec",..: 1 1 2 2 2 2 2 3 3 3 ...
## $ Location : Factor w/ 3 levels "4x5","Uva_1m2",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ Pocillopora: num 57.28 71.659 0.242 0.62 73.07 ...
## $ Year_F : Factor w/ 29 levels "1980","1983",..: 27 28 3 4 25 26 29 1 3 9 ...
## $ Date : Date, format: "2016-04-15" "2017-04-15" ... #write.csv(aggr.location,
# "Outputs/Pocillopora_mean_by_dataset.csv",
# row.names = F)Stats Pocillopora for conceptual model (pooled datasets)
Pocillopora (model 1)
This model includes aggregated data from Chiriqui
- Aggregated by location (Dataset)
- YEAR is a continuous variable
Location (Dataset) as a random factor
Model is significant, but ignores high cover pre-1982
Data does not look normally distributed, which is ok, since the coral cover cannot be linear (Year as continuous), unless pre-1982 is removed?
** Do I need to change the intercept options?**
# # All years 1980_2018
# model1 <- lme(
# Pocillopora ~ -1 + YEAR, random = ~1|Location, data=aggr.location)
# summary(model1)
# anova(model1)
#
# plot(ranef(model1)) # Symmetrical scatter effects around zero?
# plot(model1) # plot residuals vs fitted
# resnorm1 <- resid(model1)
# hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
# coef.m1 <- as.data.frame(coef(summary(model1))) # Coefficients of the model
#
# plot(model1, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
# plot(model1, Pocillopora ~ fitted(.), abline = c(0,1))
#-----
model1 <- lme(
Pocillopora ~ YEAR, random = ~1|Location, data=aggr.location)
summary(model1)## Linear mixed-effects model fit by REML
## Data: aggr.location
## AIC BIC logLik
## 733.8074 743.6711 -362.9037
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 9.141383 14.07197
##
## Fixed effects: Pocillopora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3022.5412 274.27885 85 -11.01996 0
## YEAR 1.5229 0.13718 85 11.10184 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.4302381 -0.6011531 -0.2493395 0.4524815 5.3743803
##
## Number of Observations: 89
## Number of Groups: 3 anova(model1) plot(ranef(model1)) # Symmetrical scatter effects around zero?
plot(model1) # plot residuals vs fitted
resnorm1 <- resid(model1)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model1))) # Coefficients of the model
plot(model1, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model1, Pocillopora ~ fitted(.), abline = c(0,1))
#-----
# library(lme4)
# model1 <- lmer(Pocillopora ~ YEAR + (1|Location) -1, data=aggr.location)
# summary(model1)
# anova(model1)
#
# plot(ranef(model1)) # Symmetrical scatter effects around zero?
# plot(model1) # plot residuals vs fitted
# resnorm1 <- resid(model1)
# hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
# coef.m1 <- as.data.frame(coef(summary(model1))) # Coefficients of the model
#
# plot(model1, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
# plot(model1, Pocillopora ~ fitted(.), abline = c(0,1))
Model 1 (data) plot vs (predicted values)
Model_1 <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(colour=Location))+
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80),
expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2),
expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
theme(legend.position = c(0.25, 0.8))+
labs(title="Model 1 data")Model 1
- Extract model 1 predicted values
# Create a new data frame for independent variables
NewData_1 <- expand.grid(Location=unique(aggr.location$Location),
YEAR=seq((min(aggr.location$YEAR)), (max(aggr.location$YEAR))))
pred_1 <- predict(model1 , newdata=NewData_1, level=0)
#summary(pred_1)
#length(pred_1)- Plot model predictions
# Using model data
Model1_plot <- ggplot(aggr.location,
aes(x=YEAR, y=Pocillopora, colour=Location)) +
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.3, alpha=0.5) +
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80),
expand = c(0 ,0))+
scale_x_continuous("", limits = c(1979, 2018),
breaks = seq(1980, 2018, by=2),
expand = c(0.02,0.02))+
geom_line(data=NewData_1,
aes(y=predict(model1, level=0, newdata=NewData_1)), size=2)+
labs(title="Model 1 prediction")- Compare data and predictions
Model1_All<-grid.arrange(Model_1, Model1_plot, ncol=2)
Pocillopora (model 1b: removing 1980 datapoints)
This model includes aggregated data from Chiriqui
- Aggregated by location (Dataset)
- YEAR is a continuous variable (1980 data removed)
- Location (Dataset) as a random factor
aggr.locationb<-filter(aggr.location, YEAR>1983)
summary(aggr.locationb)## YEAR Month Location Pocillopora Year_F
## Min. :1984 Mar :22 4x5 :38 Min. : 0.2145 1985 : 8
## 1st Qu.:1989 Aug :12 Uva_1m2 :18 1st Qu.: 1.5431 1984 : 7
## Median :1998 Jul :10 UvRf-Chains:28 Median :13.6481 1997 : 5
## Mean :1999 Apr : 7 Mean :20.6337 2014 : 4
## 3rd Qu.:2007 Feb : 7 3rd Qu.:33.1594 1989 : 3
## Max. :2018 Jan : 7 Max. :73.5546 1990 : 3
## (Other):19 (Other):54
## Date
## Min. :1984-06-15
## 1st Qu.:1988-12-15
## Median :1997-12-29
## Mean :1999-03-21
## 3rd Qu.:2007-07-15
## Max. :2018-08-15
## - Seems that removing the intercept is an issue…
# All years 1980_2018
model1b <- lme(
Pocillopora ~ YEAR, random = ~1| Location, data=aggr.locationb)
summary(model1b)## Linear mixed-effects model fit by REML
## Data: aggr.locationb
## AIC BIC logLik
## 640.7614 650.3883 -316.3807
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.3104 10.13543
##
## Fixed effects: Pocillopora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -3594.334 211.75305 80 -16.97418 0
## YEAR 1.808 0.10583 80 17.08316 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.0731385 -0.6259668 -0.2151230 0.5055238 2.2714197
##
## Number of Observations: 84
## Number of Groups: 3 anova(model1b) print(model1b)## Linear mixed-effects model fit by REML
## Data: aggr.locationb
## Log-restricted-likelihood: -316.3807
## Fixed: Pocillopora ~ YEAR
## (Intercept) YEAR
## -3594.334410 1.807988
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 10.3104 10.13543
##
## Number of Observations: 84
## Number of Groups: 3 plot(ranef(model1b)) # Symmetrical scatter effects around zero?
plot(model1b) # plot residuals vs fitted
resnorm1 <- resid(model1b)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model1b))) # Coefficients of the model
plot(model1b, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model1b, Pocillopora ~ fitted(.), abline = c(0,1))
Model 1b (data) plot
Model 1b
- Extract model 1b predicted values
# Create a new data frame for independent variables
NewData_1b <- expand.grid(Location=unique(aggr.locationb$Location),
YEAR=seq((min(aggr.locationb$YEAR)), (max(aggr.locationb$YEAR))))
pred_1b <- predict(model1b , newdata=NewData_1b, level=0)
#summary(pred_1)
#length(pred_1)- Plot model predictions
# Using model data
Model1_plotb <- ggplot(aggr.locationb,
aes(x=YEAR, y=Pocillopora, colour=Location)) +
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.3, alpha=0.5) +
scale_y_continuous("Pocillopora cover (%)",
breaks = seq(0, 80, by=10),
limits = c(-2, 80))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2),
expand = c(0.0,0.0))+
geom_line(data=NewData_1b,
aes(y=predict(model1b, level=0, newdata=NewData_1b)), size=2)+
labs(title="Model 1b prediction")Model 1b (data) plot vs (predicted values)
Model1b_All<-grid.arrange(Model_1b_data, Model1_plotb, ncol=2)
Pocillopora model 2 (+ multiple comparisons among years)
This model includes data from Chiriqui
- Aggregated by location
- Year is a factor
- Location as a random factor
Results:
- Model is significant
- Better normality
# All years 1980_2018
model2 <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Location, data=aggr.location)
#summary(model2)
anova(model2) plot(ranef(model2)) # Symmetrical scatter effects around zero?
plot(model2) # plot residuals vs fitted
resnorm1 <- resid(model2)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model2))) # Coefficients of the model
plot(model2, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model2, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp emmeans
Year_F.emm<-emmeans(model2, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups<-year_groups[order(year_groups$Year_F),]
year_groupsMultiple comparisons among years
- Too many lines!
Summary:
- 1980 is different from 1983-2001) -> Coral cover lose after 1981-82 ENSO
- “Recovery” by ~2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
# Multicomp emmeans glht
m.comp_Pocillopora <- glht(model2, linfct = mcp(Year_F = "Tukey"))
Model2_multipcomp<-summary(m.comp_Pocillopora, test = univariate())
Model2_multipcomp##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Pocillopora ~ -1 + Year_F, data = aggr.location,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -27.5268 10.6529 -2.584 0.009767 **
## 1984 - 1980 == 0 -51.2263 9.3265 -5.493 3.96e-08 ***
## 1985 - 1980 == 0 -48.7417 9.1672 -5.317 1.06e-07 ***
## 1986 - 1980 == 0 -43.2738 11.5586 -3.744 0.000181 ***
## 1987 - 1980 == 0 -43.0244 11.5586 -3.722 0.000197 ***
## 1988 - 1980 == 0 -42.0687 11.5586 -3.640 0.000273 ***
## 1989 - 1980 == 0 -46.4429 10.5628 -4.397 1.10e-05 ***
## 1990 - 1980 == 0 -45.3128 10.5628 -4.290 1.79e-05 ***
## 1992 - 1980 == 0 -40.1390 11.5586 -3.473 0.000515 ***
## 1993 - 1980 == 0 -39.4649 11.5586 -3.414 0.000639 ***
## 1994 - 1980 == 0 -40.4590 10.6089 -3.814 0.000137 ***
## 1995 - 1980 == 0 -34.2452 10.6089 -3.228 0.001247 **
## 1997 - 1980 == 0 -30.4038 9.7653 -3.113 0.001849 **
## 1998 - 1980 == 0 -28.9061 11.6998 -2.471 0.013487 *
## 2000 - 1980 == 0 -24.7484 10.6089 -2.333 0.019659 *
## 2001 - 1980 == 0 -23.8408 11.6987 -2.038 0.041559 *
## 2002 - 1980 == 0 -15.3993 10.6089 -1.452 0.146628
## 2003 - 1980 == 0 -13.0174 10.6089 -1.227 0.219814
## 2004 - 1980 == 0 -7.9947 11.5586 -0.692 0.489148
## 2005 - 1980 == 0 -9.4521 10.6089 -0.891 0.372954
## 2006 - 1980 == 0 -0.9493 11.6987 -0.081 0.935326
## 2007 - 1980 == 0 -6.0653 10.6089 -0.572 0.567514
## 2010 - 1980 == 0 -1.0777 10.6089 -0.102 0.919089
## 2014 - 1980 == 0 -1.8494 10.0510 -0.184 0.854010
## 2015 - 1980 == 0 3.3501 10.6089 0.316 0.752171
## 2016 - 1980 == 0 -4.3892 10.6089 -0.414 0.679075
## 2017 - 1980 == 0 10.3873 10.6089 0.979 0.327526
## 2018 - 1980 == 0 11.9443 10.6089 1.126 0.260219
## 1984 - 1983 == 0 -23.6994 8.3630 -2.834 0.004599 **
## 1985 - 1983 == 0 -21.2149 8.1285 -2.610 0.009056 **
## 1986 - 1983 == 0 -15.7469 10.6529 -1.478 0.139361
## 1987 - 1983 == 0 -15.4975 10.6529 -1.455 0.145734
## 1988 - 1983 == 0 -14.5418 10.6529 -1.365 0.172237
## 1989 - 1983 == 0 -18.9160 9.6380 -1.963 0.049686 *
## 1990 - 1983 == 0 -17.7860 9.6380 -1.845 0.064979 .
## 1992 - 1983 == 0 -12.6121 10.6529 -1.184 0.236449
## 1993 - 1983 == 0 -11.9380 10.6529 -1.121 0.262443
## 1994 - 1983 == 0 -12.9321 9.6133 -1.345 0.178549
## 1995 - 1983 == 0 -6.7184 9.6133 -0.699 0.484636
## 1997 - 1983 == 0 -2.8770 8.6234 -0.334 0.738662
## 1998 - 1983 == 0 -1.3793 10.7048 -0.129 0.897478
## 2000 - 1983 == 0 2.7785 9.6133 0.289 0.772561
## 2001 - 1983 == 0 3.6861 10.9026 0.338 0.735296
## 2002 - 1983 == 0 12.1275 9.6133 1.262 0.207116
## 2003 - 1983 == 0 14.5095 9.6133 1.509 0.131219
## 2004 - 1983 == 0 19.5322 10.6529 1.834 0.066728 .
## 2005 - 1983 == 0 18.0748 9.6133 1.880 0.060083 .
## 2006 - 1983 == 0 26.5775 10.9026 2.438 0.014780 *
## 2007 - 1983 == 0 21.4616 9.6133 2.232 0.025583 *
## 2010 - 1983 == 0 26.4492 9.6133 2.751 0.005936 **
## 2014 - 1983 == 0 25.6774 8.9340 2.874 0.004052 **
## 2015 - 1983 == 0 30.8769 9.6133 3.212 0.001319 **
## 2016 - 1983 == 0 23.1377 9.6133 2.407 0.016091 *
## 2017 - 1983 == 0 37.9141 9.6133 3.944 8.02e-05 ***
## 2018 - 1983 == 0 39.4711 9.6133 4.106 4.03e-05 ***
## 1985 - 1984 == 0 2.4845 5.9904 0.415 0.678322
## 1986 - 1984 == 0 7.9525 9.3265 0.853 0.393837
## 1987 - 1984 == 0 8.2019 9.3265 0.879 0.379175
## 1988 - 1984 == 0 9.1576 9.3265 0.982 0.326153
## 1989 - 1984 == 0 4.7834 7.9957 0.598 0.549678
## 1990 - 1984 == 0 5.9134 7.9957 0.740 0.459558
## 1992 - 1984 == 0 11.0873 9.3265 1.189 0.234520
## 1993 - 1984 == 0 11.7614 9.3265 1.261 0.207283
## 1994 - 1984 == 0 10.7673 8.1206 1.326 0.184866
## 1995 - 1984 == 0 16.9810 8.1206 2.091 0.036519 *
## 1997 - 1984 == 0 20.8224 7.0266 2.963 0.003043 **
## 1998 - 1984 == 0 22.3201 9.5824 2.329 0.019844 *
## 2000 - 1984 == 0 26.4779 8.1206 3.261 0.001112 **
## 2001 - 1984 == 0 27.3855 9.4194 2.907 0.003645 **
## 2002 - 1984 == 0 35.8269 8.1206 4.412 1.02e-05 ***
## 2003 - 1984 == 0 38.2089 8.1206 4.705 2.54e-06 ***
## 2004 - 1984 == 0 43.2316 9.3265 4.635 3.56e-06 ***
## 2005 - 1984 == 0 41.7742 8.1206 5.144 2.69e-07 ***
## 2006 - 1984 == 0 50.2770 9.4194 5.338 9.42e-08 ***
## 2007 - 1984 == 0 45.1610 8.1206 5.561 2.68e-08 ***
## 2010 - 1984 == 0 50.1486 8.1206 6.175 6.60e-10 ***
## 2014 - 1984 == 0 49.3769 7.4285 6.647 2.99e-11 ***
## 2015 - 1984 == 0 54.5763 8.1206 6.721 1.81e-11 ***
## 2016 - 1984 == 0 46.8371 8.1206 5.768 8.04e-09 ***
## 2017 - 1984 == 0 61.6136 8.1206 7.587 3.26e-14 ***
## 2018 - 1984 == 0 63.1706 8.1206 7.779 7.33e-15 ***
## 1986 - 1985 == 0 5.4680 9.1672 0.596 0.550862
## 1987 - 1985 == 0 5.7173 9.1672 0.624 0.532843
## 1988 - 1985 == 0 6.6731 9.1672 0.728 0.466658
## 1989 - 1985 == 0 2.2988 7.8290 0.294 0.769040
## 1990 - 1985 == 0 3.4289 7.8290 0.438 0.661406
## 1992 - 1985 == 0 8.6028 9.1672 0.938 0.348025
## 1993 - 1985 == 0 9.2768 9.1672 1.012 0.311559
## 1994 - 1985 == 0 8.2828 7.9369 1.044 0.296685
## 1995 - 1985 == 0 14.4965 7.9369 1.826 0.067782 .
## 1997 - 1985 == 0 18.3379 6.7999 2.697 0.007001 **
## 1998 - 1985 == 0 19.8356 9.4027 2.110 0.034896 *
## 2000 - 1985 == 0 23.9934 7.9369 3.023 0.002503 **
## 2001 - 1985 == 0 24.9010 9.2862 2.681 0.007329 **
## 2002 - 1985 == 0 33.3424 7.9369 4.201 2.66e-05 ***
## 2003 - 1985 == 0 35.7244 7.9369 4.501 6.76e-06 ***
## 2004 - 1985 == 0 40.7471 9.1672 4.445 8.80e-06 ***
## 2005 - 1985 == 0 39.2897 7.9369 4.950 7.41e-07 ***
## 2006 - 1985 == 0 47.7924 9.2862 5.147 2.65e-07 ***
## 2007 - 1985 == 0 42.6764 7.9369 5.377 7.58e-08 ***
## 2010 - 1985 == 0 47.6641 7.9369 6.005 1.91e-09 ***
## 2014 - 1985 == 0 46.8923 7.2113 6.503 7.90e-11 ***
## 2015 - 1985 == 0 52.0918 7.9369 6.563 5.27e-11 ***
## 2016 - 1985 == 0 44.3526 7.9369 5.588 2.30e-08 ***
## 2017 - 1985 == 0 59.1290 7.9369 7.450 9.35e-14 ***
## 2018 - 1985 == 0 60.6860 7.9369 7.646 2.07e-14 ***
## 1987 - 1986 == 0 0.2494 11.5586 0.022 0.982788
## 1988 - 1986 == 0 1.2051 11.5586 0.104 0.916963
## 1989 - 1986 == 0 -3.1691 10.5628 -0.300 0.764156
## 1990 - 1986 == 0 -2.0391 10.5628 -0.193 0.846925
## 1992 - 1986 == 0 3.1348 11.5586 0.271 0.786230
## 1993 - 1986 == 0 3.8089 11.5586 0.330 0.741757
## 1994 - 1986 == 0 2.8148 10.6089 0.265 0.790762
## 1995 - 1986 == 0 9.0285 10.6089 0.851 0.394753
## 1997 - 1986 == 0 12.8699 9.7653 1.318 0.187527
## 1998 - 1986 == 0 14.3676 11.6998 1.228 0.219439
## 2000 - 1986 == 0 18.5254 10.6089 1.746 0.080774 .
## 2001 - 1986 == 0 19.4330 11.6987 1.661 0.096688 .
## 2002 - 1986 == 0 27.8744 10.6089 2.627 0.008603 **
## 2003 - 1986 == 0 30.2564 10.6089 2.852 0.004345 **
## 2004 - 1986 == 0 35.2791 11.5586 3.052 0.002272 **
## 2005 - 1986 == 0 33.8217 10.6089 3.188 0.001432 **
## 2006 - 1986 == 0 42.3245 11.6987 3.618 0.000297 ***
## 2007 - 1986 == 0 37.2085 10.6089 3.507 0.000453 ***
## 2010 - 1986 == 0 42.1961 10.6089 3.977 6.97e-05 ***
## 2014 - 1986 == 0 41.4243 10.0510 4.121 3.77e-05 ***
## 2015 - 1986 == 0 46.6238 10.6089 4.395 1.11e-05 ***
## 2016 - 1986 == 0 38.8846 10.6089 3.665 0.000247 ***
## 2017 - 1986 == 0 53.6611 10.6089 5.058 4.23e-07 ***
## 2018 - 1986 == 0 55.2180 10.6089 5.205 1.94e-07 ***
## 1988 - 1987 == 0 0.9557 11.5586 0.083 0.934101
## 1989 - 1987 == 0 -3.4185 10.5628 -0.324 0.746214
## 1990 - 1987 == 0 -2.2885 10.5628 -0.217 0.828480
## 1992 - 1987 == 0 2.8854 11.5586 0.250 0.802869
## 1993 - 1987 == 0 3.5595 11.5586 0.308 0.758118
## 1994 - 1987 == 0 2.5654 10.6089 0.242 0.808923
## 1995 - 1987 == 0 8.7791 10.6089 0.828 0.407940
## 1997 - 1987 == 0 12.6206 9.7653 1.292 0.196221
## 1998 - 1987 == 0 14.1182 11.6998 1.207 0.227545
## 2000 - 1987 == 0 18.2760 10.6089 1.723 0.084942 .
## 2001 - 1987 == 0 19.1836 11.6987 1.640 0.101045
## 2002 - 1987 == 0 27.6250 10.6089 2.604 0.009216 **
## 2003 - 1987 == 0 30.0070 10.6089 2.828 0.004677 **
## 2004 - 1987 == 0 35.0297 11.5586 3.031 0.002441 **
## 2005 - 1987 == 0 33.5723 10.6089 3.165 0.001553 **
## 2006 - 1987 == 0 42.0751 11.6987 3.597 0.000322 ***
## 2007 - 1987 == 0 36.9591 10.6089 3.484 0.000494 ***
## 2010 - 1987 == 0 41.9467 10.6089 3.954 7.69e-05 ***
## 2014 - 1987 == 0 41.1750 10.0510 4.097 4.19e-05 ***
## 2015 - 1987 == 0 46.3744 10.6089 4.371 1.24e-05 ***
## 2016 - 1987 == 0 38.6352 10.6089 3.642 0.000271 ***
## 2017 - 1987 == 0 53.4117 10.6089 5.035 4.79e-07 ***
## 2018 - 1987 == 0 54.9687 10.6089 5.181 2.20e-07 ***
## 1989 - 1988 == 0 -4.3742 10.5628 -0.414 0.678789
## 1990 - 1988 == 0 -3.2442 10.5628 -0.307 0.758742
## 1992 - 1988 == 0 1.9297 11.5586 0.167 0.867410
## 1993 - 1988 == 0 2.6038 11.5586 0.225 0.821772
## 1994 - 1988 == 0 1.6097 10.6089 0.152 0.879402
## 1995 - 1988 == 0 7.8234 10.6089 0.737 0.460857
## 1997 - 1988 == 0 11.6648 9.7653 1.195 0.232274
## 1998 - 1988 == 0 13.1625 11.6998 1.125 0.260581
## 2000 - 1988 == 0 17.3203 10.6089 1.633 0.102549
## 2001 - 1988 == 0 18.2279 11.6987 1.558 0.119206
## 2002 - 1988 == 0 26.6693 10.6089 2.514 0.011942 *
## 2003 - 1988 == 0 29.0513 10.6089 2.738 0.006174 **
## 2004 - 1988 == 0 34.0740 11.5586 2.948 0.003199 **
## 2005 - 1988 == 0 32.6166 10.6089 3.074 0.002109 **
## 2006 - 1988 == 0 41.1194 11.6987 3.515 0.000440 ***
## 2007 - 1988 == 0 36.0034 10.6089 3.394 0.000690 ***
## 2010 - 1988 == 0 40.9910 10.6089 3.864 0.000112 ***
## 2014 - 1988 == 0 40.2192 10.0510 4.002 6.29e-05 ***
## 2015 - 1988 == 0 45.4187 10.6089 4.281 1.86e-05 ***
## 2016 - 1988 == 0 37.6795 10.6089 3.552 0.000383 ***
## 2017 - 1988 == 0 52.4559 10.6089 4.945 7.63e-07 ***
## 2018 - 1988 == 0 54.0129 10.6089 5.091 3.56e-07 ***
## 1990 - 1989 == 0 1.1301 9.4376 0.120 0.904689
## 1992 - 1989 == 0 6.3039 10.5628 0.597 0.550638
## 1993 - 1989 == 0 6.9780 10.5628 0.661 0.508856
## 1994 - 1989 == 0 5.9839 9.5146 0.629 0.529401
## 1995 - 1989 == 0 12.1976 9.5146 1.282 0.199844
## 1997 - 1989 == 0 16.0391 8.5806 1.869 0.061591 .
## 1998 - 1989 == 0 17.5368 10.7510 1.631 0.102852
## 2000 - 1989 == 0 21.6945 9.5146 2.280 0.022599 *
## 2001 - 1989 == 0 22.6021 10.6828 2.116 0.034367 *
## 2002 - 1989 == 0 31.0436 9.5146 3.263 0.001103 **
## 2003 - 1989 == 0 33.4255 9.5146 3.513 0.000443 ***
## 2004 - 1989 == 0 38.4482 10.5628 3.640 0.000273 ***
## 2005 - 1989 == 0 36.9908 9.5146 3.888 0.000101 ***
## 2006 - 1989 == 0 45.4936 10.6828 4.259 2.06e-05 ***
## 2007 - 1989 == 0 40.3776 9.5146 4.244 2.20e-05 ***
## 2010 - 1989 == 0 45.3652 9.5146 4.768 1.86e-06 ***
## 2014 - 1989 == 0 44.5935 8.9082 5.006 5.56e-07 ***
## 2015 - 1989 == 0 49.7930 9.5146 5.233 1.66e-07 ***
## 2016 - 1989 == 0 42.0537 9.5146 4.420 9.87e-06 ***
## 2017 - 1989 == 0 56.8302 9.5146 5.973 2.33e-09 ***
## 2018 - 1989 == 0 58.3872 9.5146 6.137 8.43e-10 ***
## 1992 - 1990 == 0 5.1739 10.5628 0.490 0.624261
## 1993 - 1990 == 0 5.8480 10.5628 0.554 0.579828
## 1994 - 1990 == 0 4.8539 9.5146 0.510 0.609946
## 1995 - 1990 == 0 11.0676 9.5146 1.163 0.244738
## 1997 - 1990 == 0 14.9090 8.5806 1.738 0.082294 .
## 1998 - 1990 == 0 16.4067 10.7510 1.526 0.126993
## 2000 - 1990 == 0 20.5645 9.5146 2.161 0.030667 *
## 2001 - 1990 == 0 21.4721 10.6828 2.010 0.044436 *
## 2002 - 1990 == 0 29.9135 9.5146 3.144 0.001667 **
## 2003 - 1990 == 0 32.2955 9.5146 3.394 0.000688 ***
## 2004 - 1990 == 0 37.3182 10.5628 3.533 0.000411 ***
## 2005 - 1990 == 0 35.8608 9.5146 3.769 0.000164 ***
## 2006 - 1990 == 0 44.3635 10.6828 4.153 3.28e-05 ***
## 2007 - 1990 == 0 39.2475 9.5146 4.125 3.71e-05 ***
## 2010 - 1990 == 0 44.2352 9.5146 4.649 3.33e-06 ***
## 2014 - 1990 == 0 43.4634 8.9082 4.879 1.07e-06 ***
## 2015 - 1990 == 0 48.6629 9.5146 5.115 3.14e-07 ***
## 2016 - 1990 == 0 40.9237 9.5146 4.301 1.70e-05 ***
## 2017 - 1990 == 0 55.7001 9.5146 5.854 4.79e-09 ***
## 2018 - 1990 == 0 57.2571 9.5146 6.018 1.77e-09 ***
## 1993 - 1992 == 0 0.6741 11.5586 0.058 0.953496
## 1994 - 1992 == 0 -0.3200 10.6089 -0.030 0.975935
## 1995 - 1992 == 0 5.8937 10.6089 0.556 0.578523
## 1997 - 1992 == 0 9.7351 9.7653 0.997 0.318806
## 1998 - 1992 == 0 11.2328 11.6998 0.960 0.337012
## 2000 - 1992 == 0 15.3906 10.6089 1.451 0.146857
## 2001 - 1992 == 0 16.2982 11.6987 1.393 0.163570
## 2002 - 1992 == 0 24.7396 10.6089 2.332 0.019703 *
## 2003 - 1992 == 0 27.1216 10.6089 2.556 0.010573 *
## 2004 - 1992 == 0 32.1443 11.5586 2.781 0.005419 **
## 2005 - 1992 == 0 30.6869 10.6089 2.893 0.003821 **
## 2006 - 1992 == 0 39.1897 11.6987 3.350 0.000808 ***
## 2007 - 1992 == 0 34.0737 10.6089 3.212 0.001319 **
## 2010 - 1992 == 0 39.0613 10.6089 3.682 0.000231 ***
## 2014 - 1992 == 0 38.2895 10.0510 3.810 0.000139 ***
## 2015 - 1992 == 0 43.4890 10.6089 4.099 4.14e-05 ***
## 2016 - 1992 == 0 35.7498 10.6089 3.370 0.000752 ***
## 2017 - 1992 == 0 50.5263 10.6089 4.763 1.91e-06 ***
## 2018 - 1992 == 0 52.0832 10.6089 4.909 9.14e-07 ***
## 1994 - 1993 == 0 -0.9941 10.6089 -0.094 0.925344
## 1995 - 1993 == 0 5.2196 10.6089 0.492 0.622716
## 1997 - 1993 == 0 9.0611 9.7653 0.928 0.353466
## 1998 - 1993 == 0 10.5587 11.6998 0.902 0.366806
## 2000 - 1993 == 0 14.7165 10.6089 1.387 0.165385
## 2001 - 1993 == 0 15.6241 11.6987 1.336 0.181698
## 2002 - 1993 == 0 24.0656 10.6089 2.268 0.023303 *
## 2003 - 1993 == 0 26.4475 10.6089 2.493 0.012669 *
## 2004 - 1993 == 0 31.4702 11.5586 2.723 0.006476 **
## 2005 - 1993 == 0 30.0128 10.6089 2.829 0.004669 **
## 2006 - 1993 == 0 38.5156 11.6987 3.292 0.000994 ***
## 2007 - 1993 == 0 33.3996 10.6089 3.148 0.001642 **
## 2010 - 1993 == 0 38.3872 10.6089 3.618 0.000296 ***
## 2014 - 1993 == 0 37.6155 10.0510 3.742 0.000182 ***
## 2015 - 1993 == 0 42.8149 10.6089 4.036 5.44e-05 ***
## 2016 - 1993 == 0 35.0757 10.6089 3.306 0.000946 ***
## 2017 - 1993 == 0 49.8522 10.6089 4.699 2.61e-06 ***
## 2018 - 1993 == 0 51.4092 10.6089 4.846 1.26e-06 ***
## 1995 - 1994 == 0 6.2137 9.4376 0.658 0.510278
## 1997 - 1994 == 0 10.0552 8.4492 1.190 0.234019
## 1998 - 1994 == 0 11.5528 10.5915 1.091 0.275376
## 2000 - 1994 == 0 15.7106 9.4376 1.665 0.095974 .
## 2001 - 1994 == 0 16.6182 10.5911 1.569 0.116631
## 2002 - 1994 == 0 25.0596 9.4376 2.655 0.007924 **
## 2003 - 1994 == 0 27.4416 9.4376 2.908 0.003641 **
## 2004 - 1994 == 0 32.4643 10.6089 3.060 0.002213 **
## 2005 - 1994 == 0 31.0069 9.4376 3.285 0.001018 **
## 2006 - 1994 == 0 39.5097 10.5911 3.730 0.000191 ***
## 2007 - 1994 == 0 34.3937 9.4376 3.644 0.000268 ***
## 2010 - 1994 == 0 39.3813 9.4376 4.173 3.01e-05 ***
## 2014 - 1994 == 0 38.6096 8.8399 4.368 1.26e-05 ***
## 2015 - 1994 == 0 43.8090 9.4376 4.642 3.45e-06 ***
## 2016 - 1994 == 0 36.0698 9.4376 3.822 0.000132 ***
## 2017 - 1994 == 0 50.8463 9.4376 5.388 7.14e-08 ***
## 2018 - 1994 == 0 52.4033 9.4376 5.553 2.81e-08 ***
## 1997 - 1995 == 0 3.8414 8.4492 0.455 0.649362
## 1998 - 1995 == 0 5.3391 10.5915 0.504 0.614196
## 2000 - 1995 == 0 9.4969 9.4376 1.006 0.314277
## 2001 - 1995 == 0 10.4045 10.5911 0.982 0.325913
## 2002 - 1995 == 0 18.8459 9.4376 1.997 0.045835 *
## 2003 - 1995 == 0 21.2279 9.4376 2.249 0.024493 *
## 2004 - 1995 == 0 26.2506 10.6089 2.474 0.013346 *
## 2005 - 1995 == 0 24.7932 9.4376 2.627 0.008612 **
## 2006 - 1995 == 0 33.2959 10.5911 3.144 0.001668 **
## 2007 - 1995 == 0 28.1800 9.4376 2.986 0.002827 **
## 2010 - 1995 == 0 33.1676 9.4376 3.514 0.000441 ***
## 2014 - 1995 == 0 32.3958 8.8399 3.665 0.000248 ***
## 2015 - 1995 == 0 37.5953 9.4376 3.984 6.79e-05 ***
## 2016 - 1995 == 0 29.8561 9.4376 3.164 0.001559 **
## 2017 - 1995 == 0 44.6325 9.4376 4.729 2.25e-06 ***
## 2018 - 1995 == 0 46.1895 9.4376 4.894 9.87e-07 ***
## 1998 - 1997 == 0 1.4977 9.6863 0.155 0.877122
## 2000 - 1997 == 0 5.6555 8.4492 0.669 0.503273
## 2001 - 1997 == 0 6.5630 9.7304 0.674 0.500000
## 2002 - 1997 == 0 15.0045 8.4492 1.776 0.075759 .
## 2003 - 1997 == 0 17.3865 8.4492 2.058 0.039613 *
## 2004 - 1997 == 0 22.4092 9.7653 2.295 0.021746 *
## 2005 - 1997 == 0 20.9518 8.4492 2.480 0.013148 *
## 2006 - 1997 == 0 29.4545 9.7304 3.027 0.002469 **
## 2007 - 1997 == 0 24.3385 8.4492 2.881 0.003970 **
## 2010 - 1997 == 0 29.3262 8.4492 3.471 0.000519 ***
## 2014 - 1997 == 0 28.5544 7.7699 3.675 0.000238 ***
## 2015 - 1997 == 0 33.7539 8.4492 3.995 6.47e-05 ***
## 2016 - 1997 == 0 26.0146 8.4492 3.079 0.002077 **
## 2017 - 1997 == 0 40.7911 8.4492 4.828 1.38e-06 ***
## 2018 - 1997 == 0 42.3481 8.4492 5.012 5.38e-07 ***
## 2000 - 1998 == 0 4.1578 10.5915 0.393 0.694645
## 2001 - 1998 == 0 5.0654 11.6513 0.435 0.663746
## 2002 - 1998 == 0 13.5068 10.5915 1.275 0.202221
## 2003 - 1998 == 0 15.8888 10.5915 1.500 0.133578
## 2004 - 1998 == 0 20.9115 11.6998 1.787 0.073883 .
## 2005 - 1998 == 0 19.4541 10.5915 1.837 0.066245 .
## 2006 - 1998 == 0 27.9568 11.6513 2.399 0.016419 *
## 2007 - 1998 == 0 22.8408 10.5915 2.157 0.031043 *
## 2010 - 1998 == 0 27.8285 10.5915 2.627 0.008603 **
## 2014 - 1998 == 0 27.0567 10.0510 2.692 0.007104 **
## 2015 - 1998 == 0 32.2562 10.5915 3.045 0.002323 **
## 2016 - 1998 == 0 24.5170 10.5915 2.315 0.020625 *
## 2017 - 1998 == 0 39.2934 10.5915 3.710 0.000207 ***
## 2018 - 1998 == 0 40.8504 10.5915 3.857 0.000115 ***
## 2001 - 2000 == 0 0.9076 10.5911 0.086 0.931712
## 2002 - 2000 == 0 9.3490 9.4376 0.991 0.321872
## 2003 - 2000 == 0 11.7310 9.4376 1.243 0.213864
## 2004 - 2000 == 0 16.7537 10.6089 1.579 0.114288
## 2005 - 2000 == 0 15.2963 9.4376 1.621 0.105063
## 2006 - 2000 == 0 23.7991 10.5911 2.247 0.024635 *
## 2007 - 2000 == 0 18.6831 9.4376 1.980 0.047743 *
## 2010 - 2000 == 0 23.6707 9.4376 2.508 0.012137 *
## 2014 - 2000 == 0 22.8989 8.8399 2.590 0.009586 **
## 2015 - 2000 == 0 28.0984 9.4376 2.977 0.002908 **
## 2016 - 2000 == 0 20.3592 9.4376 2.157 0.030986 *
## 2017 - 2000 == 0 35.1356 9.4376 3.723 0.000197 ***
## 2018 - 2000 == 0 36.6926 9.4376 3.888 0.000101 ***
## 2002 - 2001 == 0 8.4414 10.5911 0.797 0.425432
## 2003 - 2001 == 0 10.8234 10.5911 1.022 0.306812
## 2004 - 2001 == 0 15.8461 11.6987 1.355 0.175570
## 2005 - 2001 == 0 14.3887 10.5911 1.359 0.174283
## 2006 - 2001 == 0 22.8915 11.5586 1.980 0.047650 *
## 2007 - 2001 == 0 17.7755 10.5911 1.678 0.093280 .
## 2010 - 2001 == 0 22.7631 10.5911 2.149 0.031613 *
## 2014 - 2001 == 0 21.9914 10.1037 2.177 0.029512 *
## 2015 - 2001 == 0 27.1908 10.5911 2.567 0.010248 *
## 2016 - 2001 == 0 19.4516 10.5911 1.837 0.066269 .
## 2017 - 2001 == 0 34.2281 10.5911 3.232 0.001230 **
## 2018 - 2001 == 0 35.7851 10.5911 3.379 0.000728 ***
## 2003 - 2002 == 0 2.3820 9.4376 0.252 0.800738
## 2004 - 2002 == 0 7.4047 10.6089 0.698 0.485198
## 2005 - 2002 == 0 5.9473 9.4376 0.630 0.528582
## 2006 - 2002 == 0 14.4500 10.5911 1.364 0.172455
## 2007 - 2002 == 0 9.3340 9.4376 0.989 0.322647
## 2010 - 2002 == 0 14.3217 9.4376 1.518 0.129135
## 2014 - 2002 == 0 13.5499 8.8399 1.533 0.125320
## 2015 - 2002 == 0 18.7494 9.4376 1.987 0.046958 *
## 2016 - 2002 == 0 11.0102 9.4376 1.167 0.243359
## 2017 - 2002 == 0 25.7866 9.4376 2.732 0.006289 **
## 2018 - 2002 == 0 27.3436 9.4376 2.897 0.003764 **
## 2004 - 2003 == 0 5.0227 10.6089 0.473 0.635898
## 2005 - 2003 == 0 3.5653 9.4376 0.378 0.705594
## 2006 - 2003 == 0 12.0681 10.5911 1.139 0.254513
## 2007 - 2003 == 0 6.9521 9.4376 0.737 0.461341
## 2010 - 2003 == 0 11.9397 9.4376 1.265 0.205825
## 2014 - 2003 == 0 11.1680 8.8399 1.263 0.206459
## 2015 - 2003 == 0 16.3674 9.4376 1.734 0.082867 .
## 2016 - 2003 == 0 8.6282 9.4376 0.914 0.360591
## 2017 - 2003 == 0 23.4047 9.4376 2.480 0.013140 *
## 2018 - 2003 == 0 24.9617 9.4376 2.645 0.008171 **
## 2005 - 2004 == 0 -1.4574 10.6089 -0.137 0.890736
## 2006 - 2004 == 0 7.0454 11.6987 0.602 0.547016
## 2007 - 2004 == 0 1.9294 10.6089 0.182 0.855690
## 2010 - 2004 == 0 6.9170 10.6089 0.652 0.514401
## 2014 - 2004 == 0 6.1453 10.0510 0.611 0.540929
## 2015 - 2004 == 0 11.3447 10.6089 1.069 0.284908
## 2016 - 2004 == 0 3.6055 10.6089 0.340 0.733966
## 2017 - 2004 == 0 18.3820 10.6089 1.733 0.083151 .
## 2018 - 2004 == 0 19.9390 10.6089 1.879 0.060183 .
## 2006 - 2005 == 0 8.5028 10.5911 0.803 0.422078
## 2007 - 2005 == 0 3.3868 9.4376 0.359 0.719700
## 2010 - 2005 == 0 8.3744 9.4376 0.887 0.374892
## 2014 - 2005 == 0 7.6026 8.8399 0.860 0.389767
## 2015 - 2005 == 0 12.8021 9.4376 1.357 0.174938
## 2016 - 2005 == 0 5.0629 9.4376 0.536 0.591641
## 2017 - 2005 == 0 19.8394 9.4376 2.102 0.035538 *
## 2018 - 2005 == 0 21.3963 9.4376 2.267 0.023381 *
## 2007 - 2006 == 0 -5.1160 10.5911 -0.483 0.629062
## 2010 - 2006 == 0 -0.1284 10.5911 -0.012 0.990330
## 2014 - 2006 == 0 -0.9001 10.1037 -0.089 0.929011
## 2015 - 2006 == 0 4.2994 10.5911 0.406 0.684786
## 2016 - 2006 == 0 -3.4399 10.5911 -0.325 0.745339
## 2017 - 2006 == 0 11.3366 10.5911 1.070 0.284444
## 2018 - 2006 == 0 12.8936 10.5911 1.217 0.223452
## 2010 - 2007 == 0 4.9876 9.4376 0.528 0.597161
## 2014 - 2007 == 0 4.2159 8.8399 0.477 0.633422
## 2015 - 2007 == 0 9.4154 9.4376 0.998 0.318450
## 2016 - 2007 == 0 1.6761 9.4376 0.178 0.859037
## 2017 - 2007 == 0 16.4526 9.4376 1.743 0.081279 .
## 2018 - 2007 == 0 18.0096 9.4376 1.908 0.056354 .
## 2014 - 2010 == 0 -0.7718 8.8399 -0.087 0.930429
## 2015 - 2010 == 0 4.4277 9.4376 0.469 0.638955
## 2016 - 2010 == 0 -3.3115 9.4376 -0.351 0.725672
## 2017 - 2010 == 0 11.4650 9.4376 1.215 0.224433
## 2018 - 2010 == 0 13.0220 9.4376 1.380 0.167648
## 2015 - 2014 == 0 5.1995 8.8399 0.588 0.556408
## 2016 - 2014 == 0 -2.5398 8.8399 -0.287 0.773876
## 2017 - 2014 == 0 12.2367 8.8399 1.384 0.166277
## 2018 - 2014 == 0 13.7937 8.8399 1.560 0.118666
## 2016 - 2015 == 0 -7.7392 9.4376 -0.820 0.412189
## 2017 - 2015 == 0 7.0372 9.4376 0.746 0.455871
## 2018 - 2015 == 0 8.5942 9.4376 0.911 0.362484
## 2017 - 2016 == 0 14.7765 9.4376 1.566 0.117416
## 2018 - 2016 == 0 16.3335 9.4376 1.731 0.083507 .
## 2018 - 2017 == 0 1.5570 9.4376 0.165 0.868961
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Model 2 plot (data)
Model2_data <- ggplot(aggr.location, aes(x=YEAR, y=Pocillopora)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.8, alpha=0.5) +
stat_summary(fun.y=mean, geom="line", colour="gray")+
scale_y_continuous("Pocillopora sp. cover (%)", limits = c(-2, 80),
breaks = seq(-0, 80, by=10),
expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2), expand = c(0,0))+
annotate("rect", xmin = 1983, xmax = 1984,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997.5, xmax = 1998.5,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015.5, xmax = 2016.5,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
#ggtitle("Model 2 data")+
theme(legend.position = c(0.25, 0.8))
#ggsave(file="Outputs/Fig_1.svg", plot=Model2_data, width=7, height=4.5)Model 2 (predicted values)
- Extract model 2 predicted values
# Option 1
# Create a new data frame for independent variables
NewData_2 <- expand.grid(Location=unique(aggr.location$Location),
Year_F=unique(aggr.location$Year_F))
pred_2 <- predict(model2 , newdata=NewData_2, re.form= ~(1|Location),
level=0)
#summary(pred_2)
#length(pred_2)
Predicted_Pocillopora<-cbind(NewData_2, pred_2)
#write.csv(Predicted_Pocillopora, "Model2Predictions.c")
# Option 2
# Effect plot
Model2_plot<-plot(emmeans(model2, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model 2 preditions") Model2_All<-grid.arrange(Model2_data, Model2_plot, ncol=2)
Aggregate data (Massives)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mas <- aggregate(Massive ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.mas$Year_F<-as.factor(aggr.location.mas$YEAR)Massives model (3)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is a continuous variable
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model3 <- lme(
Massive ~ YEAR, random = ~1|Location, data=aggr.location.mas)
summary(Model3)## Linear mixed-effects model fit by REML
## Data: aggr.location.mas
## AIC BIC logLik
## 126.818 136.6354 -59.40901
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 0.6923411 0.4240744
##
## Fixed effects: Massive ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) 0.8176158 8.409001 84 0.09723103 0.9228
## YEAR -0.0000784 0.004201 84 -0.01865474 0.9852
## Correlation:
## (Intr)
## YEAR -0.999
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.3873192 -0.5307017 -0.3106093 0.3116354 3.6839769
##
## Number of Observations: 88
## Number of Groups: 3 anova(Model3) #plot(ranef(Model3)) # Symmetrical scatter effects around zero?
#plot(Model3) # plot residuals vs fitted
#resnorm1 <- resid(Model3)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model3))) # Coefficients of the model
#plot(Model3, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model3, Massive ~ fitted(.), abline = c(0,1))Model 3 plot (Massives, non-significant)
Massives model 4 (+ multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
- Model is significant*
# All years 1980_2018
Model4 <- lme(
Massive ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mas)
#summary(Model4)
anova(Model4) plot(ranef(Model4)) # Symmetrical scatter effects around zero?
plot(Model4) # plot residuals vs fitted
resnorm1 <- resid(Model4)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model4))) # Coefficients of the model
plot(Model4, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model4, Massive ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(Model4, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups<-year_groups[order(year_groups$Year_F),]
year_groupsMultiple comparisons among years
Summary:
- 1980 is different from every year (1983-2018) -> Non-Pocillopora coral cover loss after 1981-82 ENSO has not recovered to pre-1982 values
- 1994-1997 artifact differences by incorporating Uva1m2?
- 1997 marginally different from 1998 (p=0.06)
- 1997 different from 1999-2018 (p<0.05), except 2004-2006 -> Massive coral cover lose after 1997-98 ENSO has not recovered to pre-1997 values
m.comp_Massive <- glht(Model4, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_Massive, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = Massive ~ -1 + Year_F, data = aggr.location.mas,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -1.5981735 0.4161884 -3.840 0.000123 ***
## 1984 - 1980 == 0 -1.7098030 0.3936957 -4.343 1.41e-05 ***
## 1985 - 1980 == 0 -1.7104907 0.3887756 -4.400 1.08e-05 ***
## 1986 - 1980 == 0 -1.6840729 0.4439435 -3.793 0.000149 ***
## 1987 - 1980 == 0 -1.6134226 0.4439435 -3.634 0.000279 ***
## 1988 - 1980 == 0 -1.6506134 0.4439435 -3.718 0.000201 ***
## 1989 - 1980 == 0 -1.6880286 0.4209061 -4.010 6.06e-05 ***
## 1990 - 1980 == 0 -1.6863556 0.4209061 -4.006 6.16e-05 ***
## 1992 - 1980 == 0 -1.5621779 0.4439435 -3.519 0.000433 ***
## 1993 - 1980 == 0 -1.3730574 0.4439435 -3.093 0.001982 **
## 1994 - 1980 == 0 -1.0207870 0.4202995 -2.429 0.015153 *
## 1995 - 1980 == 0 -0.7406507 0.4202995 -1.762 0.078036 .
## 1997 - 1980 == 0 -0.8868720 0.3988428 -2.224 0.026174 *
## 1998 - 1980 == 0 -1.4535131 0.4451828 -3.265 0.001095 **
## 2000 - 1980 == 0 -1.4398855 0.4202995 -3.426 0.000613 ***
## 2001 - 1980 == 0 -1.4992969 0.4501133 -3.331 0.000866 ***
## 2002 - 1980 == 0 -1.4004362 0.4202995 -3.332 0.000862 ***
## 2003 - 1980 == 0 -1.4144354 0.4202995 -3.365 0.000765 ***
## 2004 - 1980 == 0 -1.1035111 0.4439435 -2.486 0.012930 *
## 2005 - 1980 == 0 -1.3927795 0.4202995 -3.314 0.000920 ***
## 2006 - 1980 == 0 -1.2553504 0.4501133 -2.789 0.005288 **
## 2007 - 1980 == 0 -1.4130870 0.4202995 -3.362 0.000774 ***
## 2010 - 1980 == 0 -1.4128769 0.4202995 -3.362 0.000775 ***
## 2014 - 1980 == 0 -1.4734259 0.4053657 -3.635 0.000278 ***
## 2015 - 1980 == 0 -1.4309372 0.4202995 -3.405 0.000663 ***
## 2016 - 1980 == 0 -1.7594832 0.4202995 -4.186 2.84e-05 ***
## 2017 - 1980 == 0 -1.5731163 0.4202995 -3.743 0.000182 ***
## 2018 - 1980 == 0 -1.6500693 0.4202995 -3.926 8.64e-05 ***
## 1984 - 1983 == 0 -0.1116295 0.2615147 -0.427 0.669483
## 1985 - 1983 == 0 -0.1123172 0.2540474 -0.442 0.658409
## 1986 - 1983 == 0 -0.0858994 0.3323844 -0.258 0.796072
## 1987 - 1983 == 0 -0.0152491 0.3323844 -0.046 0.963408
## 1988 - 1983 == 0 -0.0524399 0.3323844 -0.158 0.874639
## 1989 - 1983 == 0 -0.0898550 0.3009245 -0.299 0.765248
## 1990 - 1983 == 0 -0.0881820 0.3009245 -0.293 0.769494
## 1992 - 1983 == 0 0.0359956 0.3323844 0.108 0.913762
## 1993 - 1983 == 0 0.2251161 0.3323844 0.677 0.498231
## 1994 - 1983 == 0 0.5773865 0.3000755 1.924 0.054337 .
## 1995 - 1983 == 0 0.8575228 0.3000755 2.858 0.004267 **
## 1997 - 1983 == 0 0.7113015 0.2692010 2.642 0.008235 **
## 1998 - 1983 == 0 0.1446604 0.3340379 0.433 0.664967
## 2000 - 1983 == 0 0.1582881 0.3000755 0.527 0.597851
## 2001 - 1983 == 0 0.0988766 0.3405812 0.290 0.771574
## 2002 - 1983 == 0 0.1977373 0.3000755 0.659 0.509922
## 2003 - 1983 == 0 0.1837381 0.3000755 0.612 0.540335
## 2004 - 1983 == 0 0.4946625 0.3323844 1.488 0.136692
## 2005 - 1983 == 0 0.2053940 0.3000755 0.684 0.493676
## 2006 - 1983 == 0 0.3428231 0.3405812 1.007 0.314135
## 2007 - 1983 == 0 0.1850866 0.3000755 0.617 0.537367
## 2010 - 1983 == 0 0.1852966 0.3000755 0.617 0.536905
## 2014 - 1983 == 0 0.1247477 0.2787741 0.447 0.654524
## 2015 - 1983 == 0 0.1672363 0.3000755 0.557 0.577313
## 2016 - 1983 == 0 -0.1613096 0.3000755 -0.538 0.590878
## 2017 - 1983 == 0 0.0250572 0.3000755 0.084 0.933452
## 2018 - 1983 == 0 -0.0518958 0.3000755 -0.173 0.862697
## 1985 - 1984 == 0 -0.0006877 0.1868133 -0.004 0.997063
## 1986 - 1984 == 0 0.0257301 0.2909410 0.088 0.929529
## 1987 - 1984 == 0 0.0963804 0.2909410 0.331 0.740440
## 1988 - 1984 == 0 0.0591896 0.2909410 0.203 0.838790
## 1989 - 1984 == 0 0.0217744 0.2493674 0.087 0.930418
## 1990 - 1984 == 0 0.0234474 0.2493674 0.094 0.925087
## 1992 - 1984 == 0 0.1476250 0.2909410 0.507 0.611870
## 1993 - 1984 == 0 0.3367455 0.2909410 1.157 0.247094
## 1994 - 1984 == 0 0.6890160 0.2534664 2.718 0.006560 **
## 1995 - 1984 == 0 0.9691523 0.2534664 3.824 0.000132 ***
## 1997 - 1984 == 0 0.8229309 0.2195423 3.748 0.000178 ***
## 1998 - 1984 == 0 0.2562899 0.2993420 0.856 0.391900
## 2000 - 1984 == 0 0.2699175 0.2534664 1.065 0.286919
## 2001 - 1984 == 0 0.2105060 0.2939450 0.716 0.473904
## 2002 - 1984 == 0 0.3093667 0.2534664 1.221 0.222259
## 2003 - 1984 == 0 0.2953676 0.2534664 1.165 0.243892
## 2004 - 1984 == 0 0.6062919 0.2909410 2.084 0.037169 *
## 2005 - 1984 == 0 0.3170234 0.2534664 1.251 0.211025
## 2006 - 1984 == 0 0.4544526 0.2939450 1.546 0.122093
## 2007 - 1984 == 0 0.2967160 0.2534664 1.171 0.241747
## 2010 - 1984 == 0 0.2969261 0.2534664 1.171 0.241413
## 2014 - 1984 == 0 0.2363771 0.2319715 1.019 0.308207
## 2015 - 1984 == 0 0.2788657 0.2534664 1.100 0.271242
## 2016 - 1984 == 0 -0.0496802 0.2534664 -0.196 0.844608
## 2017 - 1984 == 0 0.1366867 0.2534664 0.539 0.589701
## 2018 - 1984 == 0 0.0597337 0.2534664 0.236 0.813691
## 1986 - 1985 == 0 0.0264178 0.2859176 0.092 0.926383
## 1987 - 1985 == 0 0.0970681 0.2859176 0.339 0.734235
## 1988 - 1985 == 0 0.0598773 0.2859176 0.209 0.834119
## 1989 - 1985 == 0 0.0224621 0.2441385 0.092 0.926693
## 1990 - 1985 == 0 0.0241351 0.2441385 0.099 0.921251
## 1992 - 1985 == 0 0.1483128 0.2859176 0.519 0.603952
## 1993 - 1985 == 0 0.3374333 0.2859176 1.180 0.237930
## 1994 - 1985 == 0 0.6897037 0.2476758 2.785 0.005358 **
## 1995 - 1985 == 0 0.9698400 0.2476758 3.916 9.01e-05 ***
## 1997 - 1985 == 0 0.8236187 0.2123810 3.878 0.000105 ***
## 1998 - 1985 == 0 0.2569776 0.2936421 0.875 0.381498
## 2000 - 1985 == 0 0.2706052 0.2476758 1.093 0.274579
## 2001 - 1985 == 0 0.2111938 0.2897856 0.729 0.466128
## 2002 - 1985 == 0 0.3100545 0.2476758 1.252 0.210622
## 2003 - 1985 == 0 0.2960553 0.2476758 1.195 0.231957
## 2004 - 1985 == 0 0.6069796 0.2859176 2.123 0.033761 *
## 2005 - 1985 == 0 0.3177112 0.2476758 1.283 0.199573
## 2006 - 1985 == 0 0.4551403 0.2897856 1.571 0.116273
## 2007 - 1985 == 0 0.2974037 0.2476758 1.201 0.229837
## 2010 - 1985 == 0 0.2976138 0.2476758 1.202 0.229508
## 2014 - 1985 == 0 0.2370648 0.2251042 1.053 0.292280
## 2015 - 1985 == 0 0.2795535 0.2476758 1.129 0.259021
## 2016 - 1985 == 0 -0.0489924 0.2476758 -0.198 0.843195
## 2017 - 1985 == 0 0.1373744 0.2476758 0.555 0.579131
## 2018 - 1985 == 0 0.0604214 0.2476758 0.244 0.807267
## 1987 - 1986 == 0 0.0706503 0.3604297 0.196 0.844597
## 1988 - 1986 == 0 0.0334595 0.3604297 0.093 0.926037
## 1989 - 1986 == 0 -0.0039557 0.3294007 -0.012 0.990419
## 1990 - 1986 == 0 -0.0022827 0.3294007 -0.007 0.994471
## 1992 - 1986 == 0 0.1218949 0.3604297 0.338 0.735217
## 1993 - 1986 == 0 0.3110154 0.3604297 0.863 0.388191
## 1994 - 1986 == 0 0.6632859 0.3308996 2.004 0.045017 *
## 1995 - 1986 == 0 0.9434222 0.3308996 2.851 0.004357 **
## 1997 - 1986 == 0 0.7972008 0.3046486 2.617 0.008876 **
## 1998 - 1986 == 0 0.2305598 0.3650499 0.632 0.527659
## 2000 - 1986 == 0 0.2441874 0.3308996 0.738 0.460545
## 2001 - 1986 == 0 0.1847759 0.3650108 0.506 0.612702
## 2002 - 1986 == 0 0.2836366 0.3308996 0.857 0.391352
## 2003 - 1986 == 0 0.2696375 0.3308996 0.815 0.415151
## 2004 - 1986 == 0 0.5805618 0.3604297 1.611 0.107234
## 2005 - 1986 == 0 0.2912933 0.3308996 0.880 0.378693
## 2006 - 1986 == 0 0.4287225 0.3650108 1.175 0.240176
## 2007 - 1986 == 0 0.2709859 0.3308996 0.819 0.412822
## 2010 - 1986 == 0 0.2711960 0.3308996 0.820 0.412460
## 2014 - 1986 == 0 0.2106470 0.3134807 0.672 0.501608
## 2015 - 1986 == 0 0.2531356 0.3308996 0.765 0.444276
## 2016 - 1986 == 0 -0.0754103 0.3308996 -0.228 0.819728
## 2017 - 1986 == 0 0.1109566 0.3308996 0.335 0.737385
## 2018 - 1986 == 0 0.0340036 0.3308996 0.103 0.918153
## 1988 - 1987 == 0 -0.0371908 0.3604297 -0.103 0.917816
## 1989 - 1987 == 0 -0.0746060 0.3294007 -0.226 0.820820
## 1990 - 1987 == 0 -0.0729330 0.3294007 -0.221 0.824772
## 1992 - 1987 == 0 0.0512447 0.3604297 0.142 0.886941
## 1993 - 1987 == 0 0.2403652 0.3604297 0.667 0.504846
## 1994 - 1987 == 0 0.5926356 0.3308996 1.791 0.073296 .
## 1995 - 1987 == 0 0.8727719 0.3308996 2.638 0.008350 **
## 1997 - 1987 == 0 0.7265506 0.3046486 2.385 0.017085 *
## 1998 - 1987 == 0 0.1599095 0.3650499 0.438 0.661351
## 2000 - 1987 == 0 0.1735371 0.3308996 0.524 0.599972
## 2001 - 1987 == 0 0.1141257 0.3650108 0.313 0.754536
## 2002 - 1987 == 0 0.2129864 0.3308996 0.644 0.519797
## 2003 - 1987 == 0 0.1989872 0.3308996 0.601 0.547605
## 2004 - 1987 == 0 0.5099115 0.3604297 1.415 0.157147
## 2005 - 1987 == 0 0.2206431 0.3308996 0.667 0.504901
## 2006 - 1987 == 0 0.3580722 0.3650108 0.981 0.326597
## 2007 - 1987 == 0 0.2003356 0.3308996 0.605 0.544895
## 2010 - 1987 == 0 0.2005457 0.3308996 0.606 0.544474
## 2014 - 1987 == 0 0.1399967 0.3134807 0.447 0.655173
## 2015 - 1987 == 0 0.1824853 0.3308996 0.551 0.581303
## 2016 - 1987 == 0 -0.1460606 0.3308996 -0.441 0.658920
## 2017 - 1987 == 0 0.0403063 0.3308996 0.122 0.903051
## 2018 - 1987 == 0 -0.0366467 0.3308996 -0.111 0.911816
## 1989 - 1988 == 0 -0.0374152 0.3294007 -0.114 0.909566
## 1990 - 1988 == 0 -0.0357422 0.3294007 -0.109 0.913594
## 1992 - 1988 == 0 0.0884355 0.3604297 0.245 0.806177
## 1993 - 1988 == 0 0.2775560 0.3604297 0.770 0.441259
## 1994 - 1988 == 0 0.6298264 0.3308996 1.903 0.056991 .
## 1995 - 1988 == 0 0.9099627 0.3308996 2.750 0.005960 **
## 1997 - 1988 == 0 0.7637414 0.3046486 2.507 0.012177 *
## 1998 - 1988 == 0 0.1971003 0.3650499 0.540 0.589247
## 2000 - 1988 == 0 0.2107279 0.3308996 0.637 0.524233
## 2001 - 1988 == 0 0.1513165 0.3650108 0.415 0.678469
## 2002 - 1988 == 0 0.2501772 0.3308996 0.756 0.449618
## 2003 - 1988 == 0 0.2361780 0.3308996 0.714 0.475385
## 2004 - 1988 == 0 0.5471023 0.3604297 1.518 0.129035
## 2005 - 1988 == 0 0.2578339 0.3308996 0.779 0.435867
## 2006 - 1988 == 0 0.3952630 0.3650108 1.083 0.278862
## 2007 - 1988 == 0 0.2375264 0.3308996 0.718 0.472868
## 2010 - 1988 == 0 0.2377365 0.3308996 0.718 0.472477
## 2014 - 1988 == 0 0.1771875 0.3134807 0.565 0.571920
## 2015 - 1988 == 0 0.2196762 0.3308996 0.664 0.506770
## 2016 - 1988 == 0 -0.1088697 0.3308996 -0.329 0.742147
## 2017 - 1988 == 0 0.0774971 0.3308996 0.234 0.814829
## 2018 - 1988 == 0 0.0005441 0.3308996 0.002 0.998688
## 1990 - 1989 == 0 0.0016730 0.2942896 0.006 0.995464
## 1992 - 1989 == 0 0.1258506 0.3294007 0.382 0.702417
## 1993 - 1989 == 0 0.3149711 0.3294007 0.956 0.338974
## 1994 - 1989 == 0 0.6672415 0.2968099 2.248 0.024573 *
## 1995 - 1989 == 0 0.9473779 0.2968099 3.192 0.001414 **
## 1997 - 1989 == 0 0.8011565 0.2677868 2.992 0.002774 **
## 1998 - 1989 == 0 0.2345155 0.3355691 0.699 0.484640
## 2000 - 1989 == 0 0.2481431 0.2968099 0.836 0.403136
## 2001 - 1989 == 0 0.1887316 0.3333124 0.566 0.571237
## 2002 - 1989 == 0 0.2875923 0.2968099 0.969 0.332573
## 2003 - 1989 == 0 0.2735932 0.2968099 0.922 0.356644
## 2004 - 1989 == 0 0.5845175 0.3294007 1.774 0.075983 .
## 2005 - 1989 == 0 0.2952490 0.2968099 0.995 0.319862
## 2006 - 1989 == 0 0.4326781 0.3333124 1.298 0.194247
## 2007 - 1989 == 0 0.2749416 0.2968099 0.926 0.354279
## 2010 - 1989 == 0 0.2751516 0.2968099 0.927 0.353911
## 2014 - 1989 == 0 0.2146027 0.2779215 0.772 0.440014
## 2015 - 1989 == 0 0.2570913 0.2968099 0.866 0.386390
## 2016 - 1989 == 0 -0.0714546 0.2968099 -0.241 0.809755
## 2017 - 1989 == 0 0.1149123 0.2968099 0.387 0.698639
## 2018 - 1989 == 0 0.0379593 0.2968099 0.128 0.898235
## 1992 - 1990 == 0 0.1241776 0.3294007 0.377 0.706188
## 1993 - 1990 == 0 0.3132981 0.3294007 0.951 0.341546
## 1994 - 1990 == 0 0.6655686 0.2968099 2.242 0.024935 *
## 1995 - 1990 == 0 0.9457049 0.2968099 3.186 0.001441 **
## 1997 - 1990 == 0 0.7994835 0.2677868 2.986 0.002831 **
## 1998 - 1990 == 0 0.2328425 0.3355691 0.694 0.487762
## 2000 - 1990 == 0 0.2464701 0.2968099 0.830 0.406314
## 2001 - 1990 == 0 0.1870586 0.3333124 0.561 0.574654
## 2002 - 1990 == 0 0.2859193 0.2968099 0.963 0.335393
## 2003 - 1990 == 0 0.2719202 0.2968099 0.916 0.359592
## 2004 - 1990 == 0 0.5828445 0.3294007 1.769 0.076826 .
## 2005 - 1990 == 0 0.2935760 0.2968099 0.989 0.322612
## 2006 - 1990 == 0 0.4310052 0.3333124 1.293 0.195978
## 2007 - 1990 == 0 0.2732686 0.2968099 0.921 0.357215
## 2010 - 1990 == 0 0.2734787 0.2968099 0.921 0.356845
## 2014 - 1990 == 0 0.2129297 0.2779215 0.766 0.443587
## 2015 - 1990 == 0 0.2554183 0.2968099 0.861 0.389489
## 2016 - 1990 == 0 -0.0731276 0.2968099 -0.246 0.805389
## 2017 - 1990 == 0 0.1132393 0.2968099 0.382 0.702816
## 2018 - 1990 == 0 0.0362863 0.2968099 0.122 0.902698
## 1993 - 1992 == 0 0.1891205 0.3604297 0.525 0.599786
## 1994 - 1992 == 0 0.5413909 0.3308996 1.636 0.101815
## 1995 - 1992 == 0 0.8215272 0.3308996 2.483 0.013039 *
## 1997 - 1992 == 0 0.6753059 0.3046486 2.217 0.026646 *
## 1998 - 1992 == 0 0.1086648 0.3650499 0.298 0.765954
## 2000 - 1992 == 0 0.1222925 0.3308996 0.370 0.711699
## 2001 - 1992 == 0 0.0628810 0.3650108 0.172 0.863224
## 2002 - 1992 == 0 0.1617417 0.3308996 0.489 0.624988
## 2003 - 1992 == 0 0.1477425 0.3308996 0.446 0.655245
## 2004 - 1992 == 0 0.4586669 0.3604297 1.273 0.203176
## 2005 - 1992 == 0 0.1693984 0.3308996 0.512 0.608698
## 2006 - 1992 == 0 0.3068275 0.3650108 0.841 0.400573
## 2007 - 1992 == 0 0.1490910 0.3308996 0.451 0.652305
## 2010 - 1992 == 0 0.1493010 0.3308996 0.451 0.651847
## 2014 - 1992 == 0 0.0887521 0.3134807 0.283 0.777086
## 2015 - 1992 == 0 0.1312407 0.3308996 0.397 0.691649
## 2016 - 1992 == 0 -0.1973052 0.3308996 -0.596 0.550995
## 2017 - 1992 == 0 -0.0109383 0.3308996 -0.033 0.973630
## 2018 - 1992 == 0 -0.0878914 0.3308996 -0.266 0.790537
## 1994 - 1993 == 0 0.3522704 0.3308996 1.065 0.287064
## 1995 - 1993 == 0 0.6324067 0.3308996 1.911 0.055982 .
## 1997 - 1993 == 0 0.4861854 0.3046486 1.596 0.110514
## 1998 - 1993 == 0 -0.0804557 0.3650499 -0.220 0.825563
## 2000 - 1993 == 0 -0.0668280 0.3308996 -0.202 0.839949
## 2001 - 1993 == 0 -0.1262395 0.3650108 -0.346 0.729454
## 2002 - 1993 == 0 -0.0273788 0.3308996 -0.083 0.934058
## 2003 - 1993 == 0 -0.0413780 0.3308996 -0.125 0.900486
## 2004 - 1993 == 0 0.2695464 0.3604297 0.748 0.454552
## 2005 - 1993 == 0 -0.0197221 0.3308996 -0.060 0.952473
## 2006 - 1993 == 0 0.1177070 0.3650108 0.322 0.747093
## 2007 - 1993 == 0 -0.0400295 0.3308996 -0.121 0.903713
## 2010 - 1993 == 0 -0.0398195 0.3308996 -0.120 0.904216
## 2014 - 1993 == 0 -0.1003684 0.3134807 -0.320 0.748836
## 2015 - 1993 == 0 -0.0578798 0.3308996 -0.175 0.861145
## 2016 - 1993 == 0 -0.3864257 0.3308996 -1.168 0.242886
## 2017 - 1993 == 0 -0.2000589 0.3308996 -0.605 0.545451
## 2018 - 1993 == 0 -0.2770119 0.3308996 -0.837 0.402509
## 1995 - 1994 == 0 0.2801363 0.2942896 0.952 0.341144
## 1997 - 1994 == 0 0.1339150 0.2634847 0.508 0.611281
## 1998 - 1994 == 0 -0.4327261 0.3303441 -1.310 0.190221
## 2000 - 1994 == 0 -0.4190984 0.2942896 -1.424 0.154417
## 2001 - 1994 == 0 -0.4785099 0.3303297 -1.449 0.147454
## 2002 - 1994 == 0 -0.3796492 0.2942896 -1.290 0.197032
## 2003 - 1994 == 0 -0.3936484 0.2942896 -1.338 0.181020
## 2004 - 1994 == 0 -0.0827241 0.3308996 -0.250 0.802589
## 2005 - 1994 == 0 -0.3719925 0.2942896 -1.264 0.206217
## 2006 - 1994 == 0 -0.2345634 0.3303297 -0.710 0.477649
## 2007 - 1994 == 0 -0.3922999 0.2942896 -1.333 0.182519
## 2010 - 1994 == 0 -0.3920899 0.2942896 -1.332 0.182753
## 2014 - 1994 == 0 -0.4526388 0.2756729 -1.642 0.100602
## 2015 - 1994 == 0 -0.4101502 0.2942896 -1.394 0.163409
## 2016 - 1994 == 0 -0.7386961 0.2942896 -2.510 0.012070 *
## 2017 - 1994 == 0 -0.5523293 0.2942896 -1.877 0.060543 .
## 2018 - 1994 == 0 -0.6292823 0.2942896 -2.138 0.032492 *
## 1997 - 1995 == 0 -0.1462213 0.2634847 -0.555 0.578928
## 1998 - 1995 == 0 -0.7128624 0.3303441 -2.158 0.030933 *
## 2000 - 1995 == 0 -0.6992348 0.2942896 -2.376 0.017501 *
## 2001 - 1995 == 0 -0.7586462 0.3303297 -2.297 0.021640 *
## 2002 - 1995 == 0 -0.6597855 0.2942896 -2.242 0.024964 *
## 2003 - 1995 == 0 -0.6737847 0.2942896 -2.290 0.022049 *
## 2004 - 1995 == 0 -0.3628604 0.3308996 -1.097 0.272822
## 2005 - 1995 == 0 -0.6521288 0.2942896 -2.216 0.026695 *
## 2006 - 1995 == 0 -0.5146997 0.3303297 -1.558 0.119200
## 2007 - 1995 == 0 -0.6724363 0.2942896 -2.285 0.022316 *
## 2010 - 1995 == 0 -0.6722262 0.2942896 -2.284 0.022358 *
## 2014 - 1995 == 0 -0.7327752 0.2756729 -2.658 0.007857 **
## 2015 - 1995 == 0 -0.6902865 0.2942896 -2.346 0.018996 *
## 2016 - 1995 == 0 -1.0188325 0.2942896 -3.462 0.000536 ***
## 2017 - 1995 == 0 -0.8324656 0.2942896 -2.829 0.004673 **
## 2018 - 1995 == 0 -0.9094186 0.2942896 -3.090 0.002000 **
## 1998 - 1997 == 0 -0.5666411 0.3020756 -1.876 0.060679 .
## 2000 - 1997 == 0 -0.5530134 0.2634847 -2.099 0.035831 *
## 2001 - 1997 == 0 -0.6124249 0.3035334 -2.018 0.043627 *
## 2002 - 1997 == 0 -0.5135642 0.2634847 -1.949 0.051281 .
## 2003 - 1997 == 0 -0.5275634 0.2634847 -2.002 0.045257 *
## 2004 - 1997 == 0 -0.2166390 0.3046486 -0.711 0.477015
## 2005 - 1997 == 0 -0.5059075 0.2634847 -1.920 0.054850 .
## 2006 - 1997 == 0 -0.3684784 0.3035334 -1.214 0.224762
## 2007 - 1997 == 0 -0.5262149 0.2634847 -1.997 0.045810 *
## 2010 - 1997 == 0 -0.5260049 0.2634847 -1.996 0.045897 *
## 2014 - 1997 == 0 -0.5865538 0.2423115 -2.421 0.015492 *
## 2015 - 1997 == 0 -0.5440652 0.2634847 -2.065 0.038934 *
## 2016 - 1997 == 0 -0.8726111 0.2634847 -3.312 0.000927 ***
## 2017 - 1997 == 0 -0.6862443 0.2634847 -2.604 0.009201 **
## 2018 - 1997 == 0 -0.7631973 0.2634847 -2.897 0.003773 **
## 2000 - 1998 == 0 0.0136276 0.3303441 0.041 0.967094
## 2001 - 1998 == 0 -0.0457838 0.3634983 -0.126 0.899769
## 2002 - 1998 == 0 0.0530769 0.3303441 0.161 0.872352
## 2003 - 1998 == 0 0.0390777 0.3303441 0.118 0.905835
## 2004 - 1998 == 0 0.3500020 0.3650499 0.959 0.337670
## 2005 - 1998 == 0 0.0607336 0.3303441 0.184 0.854132
## 2006 - 1998 == 0 0.1981627 0.3634983 0.545 0.585647
## 2007 - 1998 == 0 0.0404261 0.3303441 0.122 0.902601
## 2010 - 1998 == 0 0.0406362 0.3303441 0.123 0.902098
## 2014 - 1998 == 0 -0.0199128 0.3134807 -0.064 0.949351
## 2015 - 1998 == 0 0.0225758 0.3303441 0.068 0.945515
## 2016 - 1998 == 0 -0.3059701 0.3303441 -0.926 0.354334
## 2017 - 1998 == 0 -0.1196032 0.3303441 -0.362 0.717310
## 2018 - 1998 == 0 -0.1965562 0.3303441 -0.595 0.551841
## 2001 - 2000 == 0 -0.0594115 0.3303297 -0.180 0.857266
## 2002 - 2000 == 0 0.0394492 0.2942896 0.134 0.893364
## 2003 - 2000 == 0 0.0254501 0.2942896 0.086 0.931085
## 2004 - 2000 == 0 0.3363744 0.3308996 1.017 0.309370
## 2005 - 2000 == 0 0.0471059 0.2942896 0.160 0.872829
## 2006 - 2000 == 0 0.1845351 0.3303297 0.559 0.576408
## 2007 - 2000 == 0 0.0267985 0.2942896 0.091 0.927444
## 2010 - 2000 == 0 0.0270086 0.2942896 0.092 0.926876
## 2014 - 2000 == 0 -0.0335404 0.2756729 -0.122 0.903162
## 2015 - 2000 == 0 0.0089482 0.2942896 0.030 0.975743
## 2016 - 2000 == 0 -0.3195977 0.2942896 -1.086 0.277480
## 2017 - 2000 == 0 -0.1332308 0.2942896 -0.453 0.650750
## 2018 - 2000 == 0 -0.2101838 0.2942896 -0.714 0.475099
## 2002 - 2001 == 0 0.0988607 0.3303297 0.299 0.764727
## 2003 - 2001 == 0 0.0848615 0.3303297 0.257 0.797256
## 2004 - 2001 == 0 0.3957859 0.3650108 1.084 0.278226
## 2005 - 2001 == 0 0.1065174 0.3303297 0.322 0.747106
## 2006 - 2001 == 0 0.2439465 0.3604297 0.677 0.498519
## 2007 - 2001 == 0 0.0862100 0.3303297 0.261 0.794107
## 2010 - 2001 == 0 0.0864200 0.3303297 0.262 0.793616
## 2014 - 2001 == 0 0.0258711 0.3152247 0.082 0.934590
## 2015 - 2001 == 0 0.0683597 0.3303297 0.207 0.836054
## 2016 - 2001 == 0 -0.2601862 0.3303297 -0.788 0.430898
## 2017 - 2001 == 0 -0.0738194 0.3303297 -0.223 0.823168
## 2018 - 2001 == 0 -0.1507724 0.3303297 -0.456 0.648081
## 2003 - 2002 == 0 -0.0139992 0.2942896 -0.048 0.962059
## 2004 - 2002 == 0 0.2969252 0.3308996 0.897 0.369544
## 2005 - 2002 == 0 0.0076567 0.2942896 0.026 0.979243
## 2006 - 2002 == 0 0.1450858 0.3303297 0.439 0.660506
## 2007 - 2002 == 0 -0.0126507 0.2942896 -0.043 0.965712
## 2010 - 2002 == 0 -0.0124407 0.2942896 -0.042 0.966281
## 2014 - 2002 == 0 -0.0729896 0.2756729 -0.265 0.791187
## 2015 - 2002 == 0 -0.0305010 0.2942896 -0.104 0.917453
## 2016 - 2002 == 0 -0.3590469 0.2942896 -1.220 0.222447
## 2017 - 2002 == 0 -0.1726801 0.2942896 -0.587 0.557359
## 2018 - 2002 == 0 -0.2496331 0.2942896 -0.848 0.396295
## 2004 - 2003 == 0 0.3109243 0.3308996 0.940 0.347406
## 2005 - 2003 == 0 0.0216559 0.2942896 0.074 0.941339
## 2006 - 2003 == 0 0.1590850 0.3303297 0.482 0.630094
## 2007 - 2003 == 0 0.0013484 0.2942896 0.005 0.996344
## 2010 - 2003 == 0 0.0015585 0.2942896 0.005 0.995775
## 2014 - 2003 == 0 -0.0589905 0.2756729 -0.214 0.830557
## 2015 - 2003 == 0 -0.0165019 0.2942896 -0.056 0.955283
## 2016 - 2003 == 0 -0.3450478 0.2942896 -1.172 0.241006
## 2017 - 2003 == 0 -0.1586809 0.2942896 -0.539 0.589749
## 2018 - 2003 == 0 -0.2356339 0.2942896 -0.801 0.423313
## 2005 - 2004 == 0 -0.2892685 0.3308996 -0.874 0.382016
## 2006 - 2004 == 0 -0.1518393 0.3650108 -0.416 0.677420
## 2007 - 2004 == 0 -0.3095759 0.3308996 -0.936 0.349501
## 2010 - 2004 == 0 -0.3093658 0.3308996 -0.935 0.349828
## 2014 - 2004 == 0 -0.3699148 0.3134807 -1.180 0.237991
## 2015 - 2004 == 0 -0.3274262 0.3308996 -0.990 0.322417
## 2016 - 2004 == 0 -0.6559721 0.3308996 -1.982 0.047436 *
## 2017 - 2004 == 0 -0.4696052 0.3308996 -1.419 0.155847
## 2018 - 2004 == 0 -0.5465582 0.3308996 -1.652 0.098589 .
## 2006 - 2005 == 0 0.1374291 0.3303297 0.416 0.677384
## 2007 - 2005 == 0 -0.0203074 0.2942896 -0.069 0.944986
## 2010 - 2005 == 0 -0.0200974 0.2942896 -0.068 0.945554
## 2014 - 2005 == 0 -0.0806463 0.2756729 -0.293 0.769871
## 2015 - 2005 == 0 -0.0381577 0.2942896 -0.130 0.896835
## 2016 - 2005 == 0 -0.3667036 0.2942896 -1.246 0.212741
## 2017 - 2005 == 0 -0.1803368 0.2942896 -0.613 0.540017
## 2018 - 2005 == 0 -0.2572898 0.2942896 -0.874 0.381969
## 2007 - 2006 == 0 -0.1577366 0.3303297 -0.478 0.632997
## 2010 - 2006 == 0 -0.1575265 0.3303297 -0.477 0.633450
## 2014 - 2006 == 0 -0.2180754 0.3152247 -0.692 0.489057
## 2015 - 2006 == 0 -0.1755868 0.3303297 -0.532 0.595038
## 2016 - 2006 == 0 -0.5041327 0.3303297 -1.526 0.126972
## 2017 - 2006 == 0 -0.3177659 0.3303297 -0.962 0.336067
## 2018 - 2006 == 0 -0.3947189 0.3303297 -1.195 0.232117
## 2010 - 2007 == 0 0.0002101 0.2942896 0.001 0.999431
## 2014 - 2007 == 0 -0.0603389 0.2756729 -0.219 0.826745
## 2015 - 2007 == 0 -0.0178503 0.2942896 -0.061 0.951634
## 2016 - 2007 == 0 -0.3463962 0.2942896 -1.177 0.239172
## 2017 - 2007 == 0 -0.1600293 0.2942896 -0.544 0.586592
## 2018 - 2007 == 0 -0.2369823 0.2942896 -0.805 0.420664
## 2014 - 2010 == 0 -0.0605489 0.2756729 -0.220 0.826151
## 2015 - 2010 == 0 -0.0180603 0.2942896 -0.061 0.951065
## 2016 - 2010 == 0 -0.3466062 0.2942896 -1.178 0.238887
## 2017 - 2010 == 0 -0.1602394 0.2942896 -0.544 0.586101
## 2018 - 2010 == 0 -0.2371924 0.2942896 -0.806 0.420253
## 2015 - 2014 == 0 0.0424886 0.2756729 0.154 0.877510
## 2016 - 2014 == 0 -0.2860573 0.2756729 -1.038 0.299424
## 2017 - 2014 == 0 -0.0996904 0.2756729 -0.362 0.717632
## 2018 - 2014 == 0 -0.1766434 0.2756729 -0.641 0.521671
## 2016 - 2015 == 0 -0.3285459 0.2942896 -1.116 0.264250
## 2017 - 2015 == 0 -0.1421790 0.2942896 -0.483 0.629006
## 2018 - 2015 == 0 -0.2191321 0.2942896 -0.745 0.456505
## 2017 - 2016 == 0 0.1863669 0.2942896 0.633 0.526553
## 2018 - 2016 == 0 0.1094139 0.2942896 0.372 0.710049
## 2018 - 2017 == 0 -0.0769530 0.2942896 -0.261 0.793717
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)Model 4 plot (Massives, significant)
Model4_All<-grid.arrange(massives_plot, model4_plot, ncol=2)
Aggregate data (Millepora)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.mill <- aggregate(Millepora ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.mill$Year_F<-as.factor(aggr.location.mill$YEAR)Millepora model (5)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR is continuous
- Location as a random factor
Model is NOT significant
# All years 1980_2018
Model5 <- lme(Millepora ~ YEAR, random = ~1|Location, data=aggr.location.mill)
summary(Model5)## Linear mixed-effects model fit by REML
## Data: aggr.location.mill
## AIC BIC logLik
## 380.9101 390.7275 -186.455
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 1.029795 1.903698
##
## Fixed effects: Millepora ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) 56.36099 37.44453 84 1.505186 0.1360
## YEAR -0.02791 0.01873 84 -1.490502 0.1398
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -0.89098680 -0.19761334 -0.11252735 0.08986138 6.63015422
##
## Number of Observations: 88
## Number of Groups: 3 anova(Model5) #plot(ranef(Model5)) # Symmetrical scatter effects around zero?
#plot(Model5) # plot residuals vs fitted
#resnorm1 <- resid(Model5)
#hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
#coef.m1 <- as.data.frame(coef(summary(Model5))) # Coefficients of the model
#plot(Model5, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
#plot(Model5, Millepora ~ fitted(.), abline = c(0,1))Millepora model 6 (multiple comparisons between years)
This model includes data from Chiriqui * aggregated by location * Year is a factor * location as a random factor
# All years 1980_2018
Model6 <- lme(
Millepora ~ -1 + Year_F, random = ~1|Location, data=aggr.location.mill)
#summary(Model6)
anova(Model6)Millepora plots (non-significant models)
Aggregate data (aal Scleractinians)
- Hierarchically aggregate by location
# Aggregate by Location
aggr.location.scl <- aggregate(All_Corals ~ YEAR+Month+Location,
FUN=mean,data=cover)
aggr.location.scl$Year_F<-as.factor(aggr.location.scl$YEAR)All scleractinians (model 7)
This model includes aggregated data from Chiriqui
- Aggregated by location
- YEAR as a continuous variable
- Location as a random factor
Model is significant
# All years 1980_2018
Model7 <- lme(All_Corals ~ YEAR, random = ~1|Location, data=aggr.location.scl)
summary(Model7)## Linear mixed-effects model fit by REML
## Data: aggr.location.scl
## AIC BIC logLik
## 736.0592 745.9228 -364.0296
##
## Random effects:
## Formula: ~1 | Location
## (Intercept) Residual
## StdDev: 9.305161 14.25379
##
## Fixed effects: All_Corals ~ YEAR
## Value Std.Error DF t-value p-value
## (Intercept) -2968.1770 277.83805 85 -10.68312 0
## YEAR 1.4963 0.13896 85 10.76830 0
## Correlation:
## (Intr)
## YEAR -1
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.4066083 -0.6279905 -0.2874973 0.4839908 5.2554719
##
## Number of Observations: 89
## Number of Groups: 3 anova(Model7) plot(ranef(Model7)) # Symmetrical scatter effects around zero?
plot(Model7) # plot residuals vs fitted
resnorm1 <- resid(Model7)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model7))) # Coefficients of the model
plot(Model7, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model7, All_Corals ~ fitted(.), abline = c(0,1))
Model 7 plot
Scleractinian_plot <- ggplot(aggr.location.scl,
aes(x=YEAR, y=All_Corals)) +
#geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
#stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(aes(fill=factor(Location)),
shape = 21, colour = "black",
size = 2, stroke = 0.8, alpha=0.5) +
geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
geom_smooth(span = 0.3, se=T, colour="darkgray")+
scale_y_continuous("Coral cover (%)", limits = c(-0.5, 80), expand = c(0,0))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1979, 2019, by=2), expand = c(0,0))+
annotate("rect", xmin = 1982, xmax = 1983,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998,
ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016,
ymin = 0, ymax = 80, alpha = .2, fill="gray")
Scleractinian_plot + theme(legend.position = c(0.25, 0.8))
Scleractinians model 8 (multiple comparisons between years)
This model includes data from Chiriqui
- Aggregated by location
- Year as a factor
- Location as a random factor
# All years 1980_2018
Model8 <- lme(
All_Corals ~ -1 + Year_F, random = ~1|Location, data=aggr.location.scl)
#summary(Model8)
anova(Model8) plot(ranef(Model8)) # Symmetrical scatter effects around zero?
plot(Model8) # plot residuals vs fitted
resnorm1 <- resid(Model8)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(Model8))) # Coefficients of the model
plot(Model8, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(Model8, All_Corals ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm_scle<-emmeans(Model8, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups_Scle<-cld(Year_F.emm_scle, by=NULL) # compact-letter display
year_groups_Scle
Model 8 plot data
Model 8 plot
# Effect plot
Model8_predictoin<-plot(emmeans(Model8, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw()+
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model 8 predictions (All scleractinians)") Model8_All<-grid.arrange(Scleractinian_plot, Model8_predictoin, ncol=2)
Summary:
Pretty much same as only Pocillopora …
- 1980 is different from 1983-2001 -> Coral cover lose after 1981-82 ENSO
- “Recovery” by 2002 (no differences between 1980 and 2002) uninterrupted until 2018 -> no significant cover loss in 1997-98 nor 2015-16
- 1997 not different from 1998, 2000, 2001, 2003
2015 not different from 2016, 2017, 2018
m.comp_sclera <- glht(Model8, linfct = mcp(Year_F = "Tukey"))
summary(m.comp_sclera, test = univariate())##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lme.formula(fixed = All_Corals ~ -1 + Year_F, data = aggr.location.scl,
## random = ~1 | Location)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1983 - 1980 == 0 -28.4449 10.9569 -2.596 0.009429 **
## 1984 - 1980 == 0 -52.4880 9.5926 -5.472 4.46e-08 ***
## 1985 - 1980 == 0 -50.0054 9.4288 -5.303 1.14e-07 ***
## 1986 - 1980 == 0 -44.5140 11.8884 -3.744 0.000181 ***
## 1987 - 1980 == 0 -44.1940 11.8884 -3.717 0.000201 ***
## 1988 - 1980 == 0 -43.2755 11.8884 -3.640 0.000272 ***
## 1989 - 1980 == 0 -47.6867 10.8642 -4.389 1.14e-05 ***
## 1990 - 1980 == 0 -46.5527 10.8642 -4.285 1.83e-05 ***
## 1992 - 1980 == 0 -41.2590 11.8884 -3.471 0.000519 ***
## 1993 - 1980 == 0 -40.3945 11.8884 -3.398 0.000679 ***
## 1994 - 1980 == 0 -40.0334 10.9116 -3.669 0.000244 ***
## 1995 - 1980 == 0 -31.1317 10.9116 -2.853 0.004330 **
## 1997 - 1980 == 0 -28.5771 10.0439 -2.845 0.004438 **
## 1998 - 1980 == 0 -30.6908 12.0336 -2.550 0.010759 *
## 2000 - 1980 == 0 -26.2621 10.9116 -2.407 0.016093 *
## 2001 - 1980 == 0 -25.6681 12.0324 -2.133 0.032904 *
## 2002 - 1980 == 0 -16.8724 10.9116 -1.546 0.122036
## 2003 - 1980 == 0 -14.5042 10.9116 -1.329 0.183767
## 2004 - 1980 == 0 -8.6560 11.8884 -0.728 0.466550
## 2005 - 1980 == 0 -10.9193 10.9116 -1.001 0.316969
## 2006 - 1980 == 0 -2.5322 12.0324 -0.210 0.833319
## 2007 - 1980 == 0 -7.5524 10.9116 -0.692 0.488844
## 2010 - 1980 == 0 -2.5647 10.9116 -0.235 0.814176
## 2014 - 1980 == 0 -3.2670 10.3377 -0.316 0.751980
## 2015 - 1980 == 0 1.8466 10.9116 0.169 0.865614
## 2016 - 1980 == 0 -6.2235 10.9116 -0.570 0.568434
## 2017 - 1980 == 0 8.7399 10.9116 0.801 0.423147
## 2018 - 1980 == 0 10.2211 10.9116 0.937 0.348903
## 1984 - 1983 == 0 -24.0431 8.6015 -2.795 0.005186 **
## 1985 - 1983 == 0 -21.5604 8.3604 -2.579 0.009912 **
## 1986 - 1983 == 0 -16.0691 10.9569 -1.467 0.142492
## 1987 - 1983 == 0 -15.7491 10.9569 -1.437 0.150613
## 1988 - 1983 == 0 -14.8306 10.9569 -1.354 0.175883
## 1989 - 1983 == 0 -19.2417 9.9129 -1.941 0.052249 .
## 1990 - 1983 == 0 -18.1077 9.9129 -1.827 0.067748 .
## 1992 - 1983 == 0 -12.8140 10.9569 -1.169 0.242202
## 1993 - 1983 == 0 -11.9496 10.9569 -1.091 0.275449
## 1994 - 1983 == 0 -11.5885 9.8875 -1.172 0.241184
## 1995 - 1983 == 0 -2.6868 9.8875 -0.272 0.785827
## 1997 - 1983 == 0 -0.1321 8.8694 -0.015 0.988114
## 1998 - 1983 == 0 -2.2459 11.0101 -0.204 0.838367
## 2000 - 1983 == 0 2.1828 9.8875 0.221 0.825274
## 2001 - 1983 == 0 2.7769 11.2135 0.248 0.804418
## 2002 - 1983 == 0 11.5725 9.8875 1.170 0.241832
## 2003 - 1983 == 0 13.9407 9.8875 1.410 0.158559
## 2004 - 1983 == 0 19.7889 10.9569 1.806 0.070906 .
## 2005 - 1983 == 0 17.5257 9.8875 1.773 0.076311 .
## 2006 - 1983 == 0 25.9128 11.2135 2.311 0.020841 *
## 2007 - 1983 == 0 20.8925 9.8875 2.113 0.034599 *
## 2010 - 1983 == 0 25.8803 9.8875 2.617 0.008858 **
## 2014 - 1983 == 0 25.1779 9.1889 2.740 0.006143 **
## 2015 - 1983 == 0 30.2915 9.8875 3.064 0.002187 **
## 2016 - 1983 == 0 22.2214 9.8875 2.247 0.024613 *
## 2017 - 1983 == 0 37.1848 9.8875 3.761 0.000169 ***
## 2018 - 1983 == 0 38.6660 9.8875 3.911 9.21e-05 ***
## 1985 - 1984 == 0 2.4826 6.1613 0.403 0.686993
## 1986 - 1984 == 0 7.9740 9.5926 0.831 0.405822
## 1987 - 1984 == 0 8.2940 9.5926 0.865 0.387243
## 1988 - 1984 == 0 9.2125 9.5926 0.960 0.336865
## 1989 - 1984 == 0 4.8014 8.2239 0.584 0.559334
## 1990 - 1984 == 0 5.9353 8.2239 0.722 0.470465
## 1992 - 1984 == 0 11.2290 9.5926 1.171 0.241762
## 1993 - 1984 == 0 12.0935 9.5926 1.261 0.207412
## 1994 - 1984 == 0 12.4546 8.3522 1.491 0.135918
## 1995 - 1984 == 0 21.3563 8.3522 2.557 0.010559 *
## 1997 - 1984 == 0 23.9110 7.2269 3.309 0.000938 ***
## 1998 - 1984 == 0 21.7972 9.8557 2.212 0.026992 *
## 2000 - 1984 == 0 26.2259 8.3522 3.140 0.001690 **
## 2001 - 1984 == 0 26.8199 9.6880 2.768 0.005634 **
## 2002 - 1984 == 0 35.6156 8.3522 4.264 2.01e-05 ***
## 2003 - 1984 == 0 37.9838 8.3522 4.548 5.42e-06 ***
## 2004 - 1984 == 0 43.8320 9.5926 4.569 4.89e-06 ***
## 2005 - 1984 == 0 41.5688 8.3522 4.977 6.46e-07 ***
## 2006 - 1984 == 0 49.9558 9.6880 5.156 2.52e-07 ***
## 2007 - 1984 == 0 44.9356 8.3522 5.380 7.45e-08 ***
## 2010 - 1984 == 0 49.9233 8.3522 5.977 2.27e-09 ***
## 2014 - 1984 == 0 49.2210 7.6403 6.442 1.18e-10 ***
## 2015 - 1984 == 0 54.3346 8.3522 6.505 7.75e-11 ***
## 2016 - 1984 == 0 46.2645 8.3522 5.539 3.04e-08 ***
## 2017 - 1984 == 0 61.2279 8.3522 7.331 2.29e-13 ***
## 2018 - 1984 == 0 62.7091 8.3522 7.508 6.00e-14 ***
## 1986 - 1985 == 0 5.4914 9.4288 0.582 0.560293
## 1987 - 1985 == 0 5.8114 9.4288 0.616 0.537667
## 1988 - 1985 == 0 6.7299 9.4288 0.714 0.475376
## 1989 - 1985 == 0 2.3187 8.0524 0.288 0.773383
## 1990 - 1985 == 0 3.4527 8.0524 0.429 0.668083
## 1992 - 1985 == 0 8.7464 9.4288 0.928 0.353602
## 1993 - 1985 == 0 9.6109 9.4288 1.019 0.308055
## 1994 - 1985 == 0 9.9720 8.1634 1.222 0.221877
## 1995 - 1985 == 0 18.8737 8.1634 2.312 0.020778 *
## 1997 - 1985 == 0 21.4283 6.9938 3.064 0.002185 **
## 1998 - 1985 == 0 19.3146 9.6709 1.997 0.045804 *
## 2000 - 1985 == 0 23.7433 8.1634 2.909 0.003631 **
## 2001 - 1985 == 0 24.3373 9.5511 2.548 0.010831 *
## 2002 - 1985 == 0 33.1330 8.1634 4.059 4.93e-05 ***
## 2003 - 1985 == 0 35.5012 8.1634 4.349 1.37e-05 ***
## 2004 - 1985 == 0 41.3494 9.4288 4.385 1.16e-05 ***
## 2005 - 1985 == 0 39.0861 8.1634 4.788 1.68e-06 ***
## 2006 - 1985 == 0 47.4732 9.5511 4.970 6.68e-07 ***
## 2007 - 1985 == 0 42.4530 8.1634 5.200 1.99e-07 ***
## 2010 - 1985 == 0 47.4407 8.1634 5.811 6.19e-09 ***
## 2014 - 1985 == 0 46.7384 7.4170 6.301 2.95e-10 ***
## 2015 - 1985 == 0 51.8520 8.1634 6.352 2.13e-10 ***
## 2016 - 1985 == 0 43.7819 8.1634 5.363 8.18e-08 ***
## 2017 - 1985 == 0 58.7453 8.1634 7.196 6.19e-13 ***
## 2018 - 1985 == 0 60.2265 8.1634 7.378 1.61e-13 ***
## 1987 - 1986 == 0 0.3200 11.8884 0.027 0.978526
## 1988 - 1986 == 0 1.2385 11.8884 0.104 0.917029
## 1989 - 1986 == 0 -3.1727 10.8642 -0.292 0.770263
## 1990 - 1986 == 0 -2.0387 10.8642 -0.188 0.851150
## 1992 - 1986 == 0 3.2550 11.8884 0.274 0.784241
## 1993 - 1986 == 0 4.1195 11.8884 0.347 0.728956
## 1994 - 1986 == 0 4.4806 10.9116 0.411 0.681348
## 1995 - 1986 == 0 13.3823 10.9116 1.226 0.220038
## 1997 - 1986 == 0 15.9369 10.0439 1.587 0.112573
## 1998 - 1986 == 0 13.8232 12.0336 1.149 0.250672
## 2000 - 1986 == 0 18.2519 10.9116 1.673 0.094385 .
## 2001 - 1986 == 0 18.8459 12.0324 1.566 0.117287
## 2002 - 1986 == 0 27.6416 10.9116 2.533 0.011302 *
## 2003 - 1986 == 0 30.0098 10.9116 2.750 0.005955 **
## 2004 - 1986 == 0 35.8580 11.8884 3.016 0.002560 **
## 2005 - 1986 == 0 33.5947 10.9116 3.079 0.002078 **
## 2006 - 1986 == 0 41.9818 12.0324 3.489 0.000485 ***
## 2007 - 1986 == 0 36.9616 10.9116 3.387 0.000706 ***
## 2010 - 1986 == 0 41.9493 10.9116 3.844 0.000121 ***
## 2014 - 1986 == 0 41.2470 10.3377 3.990 6.61e-05 ***
## 2015 - 1986 == 0 46.3606 10.9116 4.249 2.15e-05 ***
## 2016 - 1986 == 0 38.2905 10.9116 3.509 0.000450 ***
## 2017 - 1986 == 0 53.2539 10.9116 4.880 1.06e-06 ***
## 2018 - 1986 == 0 54.7351 10.9116 5.016 5.27e-07 ***
## 1988 - 1987 == 0 0.9185 11.8884 0.077 0.938417
## 1989 - 1987 == 0 -3.4927 10.8642 -0.321 0.747843
## 1990 - 1987 == 0 -2.3587 10.8642 -0.217 0.828126
## 1992 - 1987 == 0 2.9350 11.8884 0.247 0.805002
## 1993 - 1987 == 0 3.7995 11.8884 0.320 0.749274
## 1994 - 1987 == 0 4.1606 10.9116 0.381 0.702983
## 1995 - 1987 == 0 13.0623 10.9116 1.197 0.231267
## 1997 - 1987 == 0 15.6169 10.0439 1.555 0.119976
## 1998 - 1987 == 0 13.5032 12.0336 1.122 0.261808
## 2000 - 1987 == 0 17.9319 10.9116 1.643 0.100304
## 2001 - 1987 == 0 18.5259 12.0324 1.540 0.123641
## 2002 - 1987 == 0 27.3216 10.9116 2.504 0.012283 *
## 2003 - 1987 == 0 29.6898 10.9116 2.721 0.006510 **
## 2004 - 1987 == 0 35.5380 11.8884 2.989 0.002796 **
## 2005 - 1987 == 0 33.2747 10.9116 3.049 0.002292 **
## 2006 - 1987 == 0 41.6618 12.0324 3.462 0.000535 ***
## 2007 - 1987 == 0 36.6416 10.9116 3.358 0.000785 ***
## 2010 - 1987 == 0 41.6293 10.9116 3.815 0.000136 ***
## 2014 - 1987 == 0 40.9270 10.3377 3.959 7.53e-05 ***
## 2015 - 1987 == 0 46.0406 10.9116 4.219 2.45e-05 ***
## 2016 - 1987 == 0 37.9705 10.9116 3.480 0.000502 ***
## 2017 - 1987 == 0 52.9339 10.9116 4.851 1.23e-06 ***
## 2018 - 1987 == 0 54.4151 10.9116 4.987 6.14e-07 ***
## 1989 - 1988 == 0 -4.4112 10.8642 -0.406 0.684722
## 1990 - 1988 == 0 -3.2772 10.8642 -0.302 0.762919
## 1992 - 1988 == 0 2.0165 11.8884 0.170 0.865310
## 1993 - 1988 == 0 2.8810 11.8884 0.242 0.808519
## 1994 - 1988 == 0 3.2421 10.9116 0.297 0.766374
## 1995 - 1988 == 0 12.1438 10.9116 1.113 0.265741
## 1997 - 1988 == 0 14.6984 10.0439 1.463 0.143351
## 1998 - 1988 == 0 12.5847 12.0336 1.046 0.295654
## 2000 - 1988 == 0 17.0134 10.9116 1.559 0.118948
## 2001 - 1988 == 0 17.6074 12.0324 1.463 0.143376
## 2002 - 1988 == 0 26.4031 10.9116 2.420 0.015532 *
## 2003 - 1988 == 0 28.7713 10.9116 2.637 0.008370 **
## 2004 - 1988 == 0 34.6195 11.8884 2.912 0.003591 **
## 2005 - 1988 == 0 32.3562 10.9116 2.965 0.003024 **
## 2006 - 1988 == 0 40.7433 12.0324 3.386 0.000709 ***
## 2007 - 1988 == 0 35.7231 10.9116 3.274 0.001061 **
## 2010 - 1988 == 0 40.7108 10.9116 3.731 0.000191 ***
## 2014 - 1988 == 0 40.0085 10.3377 3.870 0.000109 ***
## 2015 - 1988 == 0 45.1221 10.9116 4.135 3.55e-05 ***
## 2016 - 1988 == 0 37.0520 10.9116 3.396 0.000685 ***
## 2017 - 1988 == 0 52.0154 10.9116 4.767 1.87e-06 ***
## 2018 - 1988 == 0 53.4966 10.9116 4.903 9.45e-07 ***
## 1990 - 1989 == 0 1.1340 9.7068 0.117 0.906999
## 1992 - 1989 == 0 6.4277 10.8642 0.592 0.554093
## 1993 - 1989 == 0 7.2922 10.8642 0.671 0.502086
## 1994 - 1989 == 0 7.6532 9.7860 0.782 0.434180
## 1995 - 1989 == 0 16.5550 9.7860 1.692 0.090704 .
## 1997 - 1989 == 0 19.1096 8.8253 2.165 0.030364 *
## 1998 - 1989 == 0 16.9959 11.0576 1.537 0.124286
## 2000 - 1989 == 0 21.4246 9.7860 2.189 0.028575 *
## 2001 - 1989 == 0 22.0186 10.9876 2.004 0.045075 *
## 2002 - 1989 == 0 30.8143 9.7860 3.149 0.001639 **
## 2003 - 1989 == 0 33.1825 9.7860 3.391 0.000697 ***
## 2004 - 1989 == 0 39.0307 10.8642 3.593 0.000327 ***
## 2005 - 1989 == 0 36.7674 9.7860 3.757 0.000172 ***
## 2006 - 1989 == 0 45.1545 10.9876 4.110 3.96e-05 ***
## 2007 - 1989 == 0 40.1342 9.7860 4.101 4.11e-05 ***
## 2010 - 1989 == 0 45.1220 9.7860 4.611 4.01e-06 ***
## 2014 - 1989 == 0 44.4196 9.1624 4.848 1.25e-06 ***
## 2015 - 1989 == 0 49.5333 9.7860 5.062 4.16e-07 ***
## 2016 - 1989 == 0 41.4632 9.7860 4.237 2.27e-05 ***
## 2017 - 1989 == 0 56.4266 9.7860 5.766 8.12e-09 ***
## 2018 - 1989 == 0 57.9078 9.7860 5.917 3.27e-09 ***
## 1992 - 1990 == 0 5.2937 10.8642 0.487 0.626075
## 1993 - 1990 == 0 6.1582 10.8642 0.567 0.570829
## 1994 - 1990 == 0 6.5192 9.7860 0.666 0.505296
## 1995 - 1990 == 0 15.4210 9.7860 1.576 0.115068
## 1997 - 1990 == 0 17.9756 8.8253 2.037 0.041668 *
## 1998 - 1990 == 0 15.8619 11.0576 1.434 0.151437
## 2000 - 1990 == 0 20.2906 9.7860 2.073 0.038133 *
## 2001 - 1990 == 0 20.8846 10.9876 1.901 0.057335 .
## 2002 - 1990 == 0 29.6803 9.7860 3.033 0.002422 **
## 2003 - 1990 == 0 32.0485 9.7860 3.275 0.001057 **
## 2004 - 1990 == 0 37.8967 10.8642 3.488 0.000486 ***
## 2005 - 1990 == 0 35.6334 9.7860 3.641 0.000271 ***
## 2006 - 1990 == 0 44.0205 10.9876 4.006 6.17e-05 ***
## 2007 - 1990 == 0 39.0002 9.7860 3.985 6.74e-05 ***
## 2010 - 1990 == 0 43.9880 9.7860 4.495 6.96e-06 ***
## 2014 - 1990 == 0 43.2856 9.1624 4.724 2.31e-06 ***
## 2015 - 1990 == 0 48.3993 9.7860 4.946 7.58e-07 ***
## 2016 - 1990 == 0 40.3292 9.7860 4.121 3.77e-05 ***
## 2017 - 1990 == 0 55.2926 9.7860 5.650 1.60e-08 ***
## 2018 - 1990 == 0 56.7738 9.7860 5.802 6.57e-09 ***
## 1993 - 1992 == 0 0.8645 11.8884 0.073 0.942031
## 1994 - 1992 == 0 1.2256 10.9116 0.112 0.910572
## 1995 - 1992 == 0 10.1273 10.9116 0.928 0.353344
## 1997 - 1992 == 0 12.6819 10.0439 1.263 0.206713
## 1998 - 1992 == 0 10.5682 12.0336 0.878 0.379821
## 2000 - 1992 == 0 14.9969 10.9116 1.374 0.169318
## 2001 - 1992 == 0 15.5909 12.0324 1.296 0.195064
## 2002 - 1992 == 0 24.3866 10.9116 2.235 0.025422 *
## 2003 - 1992 == 0 26.7548 10.9116 2.452 0.014208 *
## 2004 - 1992 == 0 32.6030 11.8884 2.742 0.006099 **
## 2005 - 1992 == 0 30.3397 10.9116 2.781 0.005427 **
## 2006 - 1992 == 0 38.7268 12.0324 3.219 0.001288 **
## 2007 - 1992 == 0 33.7066 10.9116 3.089 0.002008 **
## 2010 - 1992 == 0 38.6943 10.9116 3.546 0.000391 ***
## 2014 - 1992 == 0 37.9920 10.3377 3.675 0.000238 ***
## 2015 - 1992 == 0 43.1056 10.9116 3.950 7.80e-05 ***
## 2016 - 1992 == 0 35.0355 10.9116 3.211 0.001323 **
## 2017 - 1992 == 0 49.9989 10.9116 4.582 4.60e-06 ***
## 2018 - 1992 == 0 51.4801 10.9116 4.718 2.38e-06 ***
## 1994 - 1993 == 0 0.3611 10.9116 0.033 0.973603
## 1995 - 1993 == 0 9.2628 10.9116 0.849 0.395940
## 1997 - 1993 == 0 11.8174 10.0439 1.177 0.239362
## 1998 - 1993 == 0 9.7037 12.0336 0.806 0.420021
## 2000 - 1993 == 0 14.1324 10.9116 1.295 0.195261
## 2001 - 1993 == 0 14.7264 12.0324 1.224 0.220991
## 2002 - 1993 == 0 23.5221 10.9116 2.156 0.031107 *
## 2003 - 1993 == 0 25.8903 10.9116 2.373 0.017657 *
## 2004 - 1993 == 0 31.7385 11.8884 2.670 0.007592 **
## 2005 - 1993 == 0 29.4752 10.9116 2.701 0.006907 **
## 2006 - 1993 == 0 37.8623 12.0324 3.147 0.001651 **
## 2007 - 1993 == 0 32.8421 10.9116 3.010 0.002614 **
## 2010 - 1993 == 0 37.8298 10.9116 3.467 0.000526 ***
## 2014 - 1993 == 0 37.1275 10.3377 3.591 0.000329 ***
## 2015 - 1993 == 0 42.2411 10.9116 3.871 0.000108 ***
## 2016 - 1993 == 0 34.1710 10.9116 3.132 0.001738 **
## 2017 - 1993 == 0 49.1344 10.9116 4.503 6.70e-06 ***
## 2018 - 1993 == 0 50.6156 10.9116 4.639 3.51e-06 ***
## 1995 - 1994 == 0 8.9017 9.7068 0.917 0.359113
## 1997 - 1994 == 0 11.4564 8.6903 1.318 0.187406
## 1998 - 1994 == 0 9.3426 10.8937 0.858 0.391104
## 2000 - 1994 == 0 13.7713 9.7068 1.419 0.155980
## 2001 - 1994 == 0 14.3653 10.8933 1.319 0.187258
## 2002 - 1994 == 0 23.1610 9.7068 2.386 0.017030 *
## 2003 - 1994 == 0 25.5292 9.7068 2.630 0.008538 **
## 2004 - 1994 == 0 31.3774 10.9116 2.876 0.004033 **
## 2005 - 1994 == 0 29.1141 9.7068 2.999 0.002706 **
## 2006 - 1994 == 0 37.5012 10.8933 3.443 0.000576 ***
## 2007 - 1994 == 0 32.4810 9.7068 3.346 0.000819 ***
## 2010 - 1994 == 0 37.4688 9.7068 3.860 0.000113 ***
## 2014 - 1994 == 0 36.7664 9.0921 4.044 5.26e-05 ***
## 2015 - 1994 == 0 41.8800 9.7068 4.314 1.60e-05 ***
## 2016 - 1994 == 0 33.8099 9.7068 3.483 0.000496 ***
## 2017 - 1994 == 0 48.7733 9.7068 5.025 5.04e-07 ***
## 2018 - 1994 == 0 50.2546 9.7068 5.177 2.25e-07 ***
## 1997 - 1995 == 0 2.5546 8.6903 0.294 0.768786
## 1998 - 1995 == 0 0.4409 10.8937 0.040 0.967716
## 2000 - 1995 == 0 4.8696 9.7068 0.502 0.615902
## 2001 - 1995 == 0 5.4636 10.8933 0.502 0.615978
## 2002 - 1995 == 0 14.2593 9.7068 1.469 0.141834
## 2003 - 1995 == 0 16.6275 9.7068 1.713 0.086718 .
## 2004 - 1995 == 0 22.4757 10.9116 2.060 0.039418 *
## 2005 - 1995 == 0 20.2124 9.7068 2.082 0.037316 *
## 2006 - 1995 == 0 28.5995 10.8933 2.625 0.008654 **
## 2007 - 1995 == 0 23.5793 9.7068 2.429 0.015135 *
## 2010 - 1995 == 0 28.5670 9.7068 2.943 0.003251 **
## 2014 - 1995 == 0 27.8647 9.0921 3.065 0.002179 **
## 2015 - 1995 == 0 32.9783 9.7068 3.397 0.000680 ***
## 2016 - 1995 == 0 24.9082 9.7068 2.566 0.010287 *
## 2017 - 1995 == 0 39.8716 9.7068 4.108 4.00e-05 ***
## 2018 - 1995 == 0 41.3528 9.7068 4.260 2.04e-05 ***
## 1998 - 1997 == 0 -2.1137 9.9627 -0.212 0.831979
## 2000 - 1997 == 0 2.3150 8.6903 0.266 0.789942
## 2001 - 1997 == 0 2.9090 10.0080 0.291 0.771307
## 2002 - 1997 == 0 11.7047 8.6903 1.347 0.178023
## 2003 - 1997 == 0 14.0729 8.6903 1.619 0.105366
## 2004 - 1997 == 0 19.9211 10.0439 1.983 0.047321 *
## 2005 - 1997 == 0 17.6578 8.6903 2.032 0.042164 *
## 2006 - 1997 == 0 26.0449 10.0080 2.602 0.009257 **
## 2007 - 1997 == 0 21.0246 8.6903 2.419 0.015549 *
## 2010 - 1997 == 0 26.0124 8.6903 2.993 0.002760 **
## 2014 - 1997 == 0 25.3101 7.9916 3.167 0.001540 **
## 2015 - 1997 == 0 30.4237 8.6903 3.501 0.000464 ***
## 2016 - 1997 == 0 22.3536 8.6903 2.572 0.010104 *
## 2017 - 1997 == 0 37.3170 8.6903 4.294 1.75e-05 ***
## 2018 - 1997 == 0 38.7982 8.6903 4.465 8.02e-06 ***
## 2000 - 1998 == 0 4.4287 10.8937 0.407 0.684347
## 2001 - 1998 == 0 5.0227 11.9837 0.419 0.675121
## 2002 - 1998 == 0 13.8184 10.8937 1.268 0.204628
## 2003 - 1998 == 0 16.1866 10.8937 1.486 0.137314
## 2004 - 1998 == 0 22.0348 12.0336 1.831 0.067084 .
## 2005 - 1998 == 0 19.7715 10.8937 1.815 0.069532 .
## 2006 - 1998 == 0 28.1586 11.9837 2.350 0.018786 *
## 2007 - 1998 == 0 23.1384 10.8937 2.124 0.033669 *
## 2010 - 1998 == 0 28.1261 10.8937 2.582 0.009827 **
## 2014 - 1998 == 0 27.4238 10.3377 2.653 0.007983 **
## 2015 - 1998 == 0 32.5374 10.8937 2.987 0.002819 **
## 2016 - 1998 == 0 24.4673 10.8937 2.246 0.024704 *
## 2017 - 1998 == 0 39.4307 10.8937 3.620 0.000295 ***
## 2018 - 1998 == 0 40.9119 10.8937 3.756 0.000173 ***
## 2001 - 2000 == 0 0.5940 10.8933 0.055 0.956513
## 2002 - 2000 == 0 9.3897 9.7068 0.967 0.333380
## 2003 - 2000 == 0 11.7579 9.7068 1.211 0.225780
## 2004 - 2000 == 0 17.6061 10.9116 1.614 0.106631
## 2005 - 2000 == 0 15.3428 9.7068 1.581 0.113965
## 2006 - 2000 == 0 23.7299 10.8933 2.178 0.029376 *
## 2007 - 2000 == 0 18.7097 9.7068 1.927 0.053921 .
## 2010 - 2000 == 0 23.6974 9.7068 2.441 0.014634 *
## 2014 - 2000 == 0 22.9951 9.0921 2.529 0.011435 *
## 2015 - 2000 == 0 28.1087 9.7068 2.896 0.003782 **
## 2016 - 2000 == 0 20.0386 9.7068 2.064 0.038982 *
## 2017 - 2000 == 0 35.0020 9.7068 3.606 0.000311 ***
## 2018 - 2000 == 0 36.4832 9.7068 3.759 0.000171 ***
## 2002 - 2001 == 0 8.7957 10.8933 0.807 0.419412
## 2003 - 2001 == 0 11.1639 10.8933 1.025 0.305437
## 2004 - 2001 == 0 17.0121 12.0324 1.414 0.157404
## 2005 - 2001 == 0 14.7488 10.8933 1.354 0.175757
## 2006 - 2001 == 0 23.1359 11.8884 1.946 0.051644 .
## 2007 - 2001 == 0 18.1157 10.8933 1.663 0.096310 .
## 2010 - 2001 == 0 23.1034 10.8933 2.121 0.033931 *
## 2014 - 2001 == 0 22.4011 10.3919 2.156 0.031113 *
## 2015 - 2001 == 0 27.5147 10.8933 2.526 0.011542 *
## 2016 - 2001 == 0 19.4446 10.8933 1.785 0.074260 .
## 2017 - 2001 == 0 34.4080 10.8933 3.159 0.001585 **
## 2018 - 2001 == 0 35.8892 10.8933 3.295 0.000986 ***
## 2003 - 2002 == 0 2.3682 9.7068 0.244 0.807251
## 2004 - 2002 == 0 8.2164 10.9116 0.753 0.451451
## 2005 - 2002 == 0 5.9531 9.7068 0.613 0.539684
## 2006 - 2002 == 0 14.3402 10.8933 1.316 0.188030
## 2007 - 2002 == 0 9.3200 9.7068 0.960 0.336983
## 2010 - 2002 == 0 14.3077 9.7068 1.474 0.140486
## 2014 - 2002 == 0 13.6054 9.0921 1.496 0.134550
## 2015 - 2002 == 0 18.7190 9.7068 1.928 0.053801 .
## 2016 - 2002 == 0 10.6489 9.7068 1.097 0.272620
## 2017 - 2002 == 0 25.6123 9.7068 2.639 0.008325 **
## 2018 - 2002 == 0 27.0935 9.7068 2.791 0.005252 **
## 2004 - 2003 == 0 5.8482 10.9116 0.536 0.591985
## 2005 - 2003 == 0 3.5849 9.7068 0.369 0.711891
## 2006 - 2003 == 0 11.9720 10.8933 1.099 0.271756
## 2007 - 2003 == 0 6.9518 9.7068 0.716 0.473886
## 2010 - 2003 == 0 11.9395 9.7068 1.230 0.218693
## 2014 - 2003 == 0 11.2372 9.0921 1.236 0.216486
## 2015 - 2003 == 0 16.3508 9.7068 1.684 0.092093 .
## 2016 - 2003 == 0 8.2807 9.7068 0.853 0.393617
## 2017 - 2003 == 0 23.2441 9.7068 2.395 0.016638 *
## 2018 - 2003 == 0 24.7253 9.7068 2.547 0.010859 *
## 2005 - 2004 == 0 -2.2633 10.9116 -0.207 0.835681
## 2006 - 2004 == 0 6.1238 12.0324 0.509 0.610792
## 2007 - 2004 == 0 1.1036 10.9116 0.101 0.919442
## 2010 - 2004 == 0 6.0913 10.9116 0.558 0.576679
## 2014 - 2004 == 0 5.3890 10.3377 0.521 0.602164
## 2015 - 2004 == 0 10.5026 10.9116 0.963 0.335790
## 2016 - 2004 == 0 2.4325 10.9116 0.223 0.823593
## 2017 - 2004 == 0 17.3959 10.9116 1.594 0.110878
## 2018 - 2004 == 0 18.8771 10.9116 1.730 0.083629 .
## 2006 - 2005 == 0 8.3871 10.8933 0.770 0.441339
## 2007 - 2005 == 0 3.3668 9.7068 0.347 0.728702
## 2010 - 2005 == 0 8.3546 9.7068 0.861 0.389408
## 2014 - 2005 == 0 7.6523 9.0921 0.842 0.399990
## 2015 - 2005 == 0 12.7659 9.7068 1.315 0.188462
## 2016 - 2005 == 0 4.6958 9.7068 0.484 0.628557
## 2017 - 2005 == 0 19.6592 9.7068 2.025 0.042838 *
## 2018 - 2005 == 0 21.1404 9.7068 2.178 0.029415 *
## 2007 - 2006 == 0 -5.0202 10.8933 -0.461 0.644901
## 2010 - 2006 == 0 -0.0325 10.8933 -0.003 0.997620
## 2014 - 2006 == 0 -0.7348 10.3919 -0.071 0.943626
## 2015 - 2006 == 0 4.3788 10.8933 0.402 0.687706
## 2016 - 2006 == 0 -3.6913 10.8933 -0.339 0.734713
## 2017 - 2006 == 0 11.2721 10.8933 1.035 0.300775
## 2018 - 2006 == 0 12.7533 10.8933 1.171 0.241700
## 2010 - 2007 == 0 4.9878 9.7068 0.514 0.607364
## 2014 - 2007 == 0 4.2854 9.0921 0.471 0.637403
## 2015 - 2007 == 0 9.3990 9.7068 0.968 0.332900
## 2016 - 2007 == 0 1.3289 9.7068 0.137 0.891106
## 2017 - 2007 == 0 16.2923 9.7068 1.678 0.093262 .
## 2018 - 2007 == 0 17.7736 9.7068 1.831 0.067096 .
## 2014 - 2010 == 0 -0.7024 9.0921 -0.077 0.938426
## 2015 - 2010 == 0 4.4113 9.7068 0.454 0.649505
## 2016 - 2010 == 0 -3.6588 9.7068 -0.377 0.706223
## 2017 - 2010 == 0 11.3046 9.7068 1.165 0.244182
## 2018 - 2010 == 0 12.7858 9.7068 1.317 0.187774
## 2015 - 2014 == 0 5.1136 9.0921 0.562 0.573827
## 2016 - 2014 == 0 -2.9565 9.0921 -0.325 0.745051
## 2017 - 2014 == 0 12.0069 9.0921 1.321 0.186639
## 2018 - 2014 == 0 13.4881 9.0921 1.484 0.137941
## 2016 - 2015 == 0 -8.0701 9.7068 -0.831 0.405757
## 2017 - 2015 == 0 6.8933 9.7068 0.710 0.477612
## 2018 - 2015 == 0 8.3745 9.7068 0.863 0.388279
## 2017 - 2016 == 0 14.9634 9.7068 1.542 0.123187
## 2018 - 2016 == 0 16.4446 9.7068 1.694 0.090241 .
## 2018 - 2017 == 0 1.4812 9.7068 0.153 0.878718
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Univariate p values reported)2. Stacked categories - Supplement? Uva Island
Only plots, not stats
Explore 4x5
Data4_5<-subset(cover, Location=="4x5")
Explore Uva chains
Data_Chain_Uva<-subset(cover, Location=="UvRf-Chains")By transect
Mean Chains
Uva_1m2
Data_Uva12<-subset(cover, Location=="Uva_1m2")By transect
Mean 1m2
Cover<-grid.arrange(Plot_45 , Plot_UvaChains, Plot_Uva1m2, ncol=1)
#ggsave(file="Outputs/Fig_S1.svg", plot=Cover, width=8, height=10)3. Supplemantary datasets (Canal del Afuera and Secas)
Import data
# Read Canal de Afuera data (Pocillopora 2014-2018)
Data_CanalAfuera <- read.csv("Data/CA_cover.csv", header=TRUE, sep = ",")
#summary(Data_CanalAfuera)
# Read Secas data (Massives 1980-2018)
Data_Chain_SECAS <- read.csv("Data/Secas_cover.csv", header=TRUE, sep = ",")
#summary(Data_Chain_SECAS)
# Read Secas + Uva data (Massives 1980-2018)
Suplementary.masssives <- read.csv("Data/Massives_cover.csv", header=TRUE, sep = ",")
#summary(Suplementary.masssives)
# Format color
FILL <-c("#C77CFF", "#F8766D", "#00BA38", "#619CFF")Pocillopora non-Uva (Canal de Afuera)
Pocillopora_CA <- ggplot(Data_CanalAfuera, aes(x=YEAR, y=Pocillopora)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
geom_point(colour="#A3A500", alpha=0.3)+
stat_summary(fun.y=mean, geom="line", colour="#A3A500") +
stat_summary(fun.y=mean, geom="point", shape=21, size=2, alpha=0.8, fill="#A3A500") +
scale_y_continuous("Canal de afuera reef \n Pocillopora cover (%)",
limits = c(-2, 90), breaks = seq(0, 100, by=20),
expand = c(0,0.1))+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2), expand = c(0,0))+
facet_grid(Location~., scales="free")+
ggtitle("a.")+
annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 80, alpha = .2, fill="gray")+
facet_grid(Location~.)
Pocillopora_CA 
- LMER model
Data_CanalAfuera$Year_F<-as.factor(Data_CanalAfuera$YEAR)
model_CA <- lme(
Pocillopora ~ -1 + Year_F, random = ~1|Transect, data=Data_CanalAfuera)
summary(model_CA)## Linear mixed-effects model fit by REML
## Data: Data_CanalAfuera
## AIC BIC logLik
## 114.7784 118.3186 -52.38918
##
## Random effects:
## Formula: ~1 | Transect
## (Intercept) Residual
## StdDev: 9.232427 4.216186
##
## Fixed effects: Pocillopora ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F2015 57.43305 4.143548 10 13.86084 0
## Year_F2016 57.00977 4.143548 10 13.75868 0
## Year_F2018 70.15725 4.143548 10 16.93169 0
## Correlation:
## Y_F2015 Y_F2016
## Year_F2016 0.827
## Year_F2018 0.827 0.827
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -1.05091857 -0.65554034 -0.05954312 0.42760030 1.72437930
##
## Number of Observations: 18
## Number of Groups: 6 anova(model_CA) plot(ranef(model_CA)) # Symmetrical scatter effects around zero?
plot(model_CA) # plot residuals vs fitted
resnorm1 <- resid(model_CA)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model_CA))) # Coefficients of the model
plot(model_CA, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model_CA, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model_CA, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups# Effect plot
plot(emmeans(model_CA, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model CA preditions")
- Summary stats Pocillopora CA
Massives Secas
Massive_Secas <- ggplot(Data_Chain_SECAS, aes(x=YEAR, y=Massive)) +
geom_boxplot(aes(group=YEAR), outlier.shape = NA) +
stat_boxplot(aes(group=YEAR), geom = 'errorbar')+
#geom_smooth(method = lm, se=FALSE, linetype = "dashed", colour="red")+
#geom_smooth(span = 0.2, se=T, colour="darkgray")+
stat_summary(fun.y=mean, geom="line") +
geom_point(aes(fill=Transect), alpha=0.5, shape=21) +
scale_y_continuous("Secas Island reef \n Non-Pocillopora scleractinians cover (%)",
limits = c(-2, 80), breaks = seq(0, 100, by=10),
expand = c(0,0.1)
)+
scale_x_continuous("", limits = c(1979, 2019),
breaks = seq(1980, 2018, by=2)#,
#expand = c(0.1,0)
)+
annotate("rect", xmin = 1982, xmax = 1983, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
annotate("rect", xmin = 1997, xmax = 1998, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
annotate("rect", xmin = 2015, xmax = 2016, ymin = 0, ymax = 70, alpha = .2, fill="gray")+
#facet_grid(Location~., scales="free_y")
ggtitle("b.")
Massive_Secas
- LMER model SECAS
Data_Chain_SECAS$Year_F<-as.factor(Data_Chain_SECAS$YEAR)
model_Secas <- lme(
Massive ~ -1 + Year_F, random = ~1|Transect, data=Data_Chain_SECAS)
summary(model_Secas)## Linear mixed-effects model fit by REML
## Data: Data_Chain_SECAS
## AIC BIC logLik
## 1734.272 1796.924 -849.1361
##
## Random effects:
## Formula: ~1 | Transect
## (Intercept) Residual
## StdDev: 0.0004912232 7.641786
##
## Fixed effects: Massive ~ -1 + Year_F
## Value Std.Error DF t-value p-value
## Year_F1975 1.891718 1.528357 231 1.237746 0.2171
## Year_F1976 0.898021 1.708755 231 0.525541 0.5997
## Year_F1977 1.621573 1.208273 231 1.342059 0.1809
## Year_F1978 1.679452 1.080712 231 1.554024 0.1215
## Year_F1980 18.183354 1.753146 231 10.371842 0.0000
## Year_F1983 0.385200 2.416545 231 0.159401 0.8735
## Year_F1997 0.225000 2.416545 231 0.093108 0.9259
## Year_F1998 0.904762 2.888324 231 0.313248 0.7544
## Year_F2000 0.000000 2.416545 231 0.000000 1.0000
## Year_F2002 0.158157 2.416545 231 0.065448 0.9479
## Year_F2003 0.500000 2.416545 231 0.206907 0.8363
## Year_F2004 0.300000 2.416545 231 0.124144 0.9013
## Year_F2005 0.200000 2.416545 231 0.082763 0.9341
## Year_F2010 1.200000 2.416545 231 0.496577 0.6200
## Year_F2015 0.264049 3.417511 231 0.077264 0.9385
## Year_F2018 0.070547 2.416545 231 0.029193 0.9767
## Correlation:
## Y_F1975 Y_F1976 Y_F1977 Y_F1978 Y_F1980 Y_F1983 Y_F1997 Y_F1998
## Year_F1976 0
## Year_F1977 0 0
## Year_F1978 0 0 0
## Year_F1980 0 0 0 0
## Year_F1983 0 0 0 0 0
## Year_F1997 0 0 0 0 0 0
## Year_F1998 0 0 0 0 0 0 0
## Year_F2000 0 0 0 0 0 0 0 0
## Year_F2002 0 0 0 0 0 0 0 0
## Year_F2003 0 0 0 0 0 0 0 0
## Year_F2004 0 0 0 0 0 0 0 0
## Year_F2005 0 0 0 0 0 0 0 0
## Year_F2010 0 0 0 0 0 0 0 0
## Year_F2015 0 0 0 0 0 0 0 0
## Year_F2018 0 0 0 0 0 0 0 0
## Y_F2000 Y_F2002 Y_F2003 Y_F2004 Y_F2005 Y_F2010 Y_F2015
## Year_F1976
## Year_F1977
## Year_F1978
## Year_F1980
## Year_F1983
## Year_F1997
## Year_F1998
## Year_F2000
## Year_F2002 0
## Year_F2003 0 0
## Year_F2004 0 0 0
## Year_F2005 0 0 0 0
## Year_F2010 0 0 0 0 0
## Year_F2015 0 0 0 0 0 0
## Year_F2018 0 0 0 0 0 0 0
##
## Standardized Within-Group Residuals:
## Min Q1 Med Q3 Max
## -2.379463717 -0.212198142 -0.075570702 -0.004047582 6.834475873
##
## Number of Observations: 256
## Number of Groups: 10 anova(model_Secas) plot(ranef(model_Secas)) # Symmetrical scatter effects around zero?
plot(model_Secas) # plot residuals vs fitted
resnorm1 <- resid(model_Secas)
hist(resnorm1, xlab = "Residuals", main = "") # are residuals normally distributed?
coef.m1 <- as.data.frame(coef(summary(model_Secas))) # Coefficients of the model
plot(model_Secas, resid(., type = "p") ~ fitted(.) | Location, abline = 0)
plot(model_Secas, Pocillopora ~ fitted(.), abline = c(0,1))
# Multicomp
Year_F.emm<-emmeans(model_Secas, ~Year_F)
#contrast(Year_F.emm, "tukey")
year_groups<-cld(Year_F.emm, by=NULL) # compact-letter display
year_groups# Effect plot
plot(emmeans(model_Secas, ~Year_F), comparisons = TRUE) +
coord_flip(xlim = NULL, ylim = NULL, expand = TRUE) + theme_bw() +
theme(axis.text.x = element_text(angle = 90)) +
ggtitle("Model Secas preditions")
- Summary stats Massives Secas
Massives Uva+Secas
Other Supplemetary figures cover
Packages used
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